Included is an up-to-date version of the service specification file used by the
MSU mail server utility program. It now lists 26 email servers; recent additions
include Bioccelerator, BioSCAN, EMBL PROSITE, SBASE, ProDom, and GCRDb.
MSU simplifies access to Internet email servers by providing a customizable menu
interface. MSU is available for UNIX and VAX systems from
{ftp,gopher,www}.embl-heidelberg.de.
--
Rainer Fuchs
EMBL Data Library
Fuchs at EMBL-Heidelberg.DE
================================================================================
############################################################
# MSU default service specification file
# Rainer Fuchs, EMBL Data Library
# Fuchs at EMBL-Heidelberg.DE
############################################################
###
# EMBL Blitz server
# 3-Dec-1993
###
service-name: EMBL BLITZ server
service-info: Ultra-fast sequence comparisons on massively parallel computer
service-addr: blitz at embl-heidelberg.de
--
help-address: blitz at embl-heidelberg.de
help-body: help
//
service-prot-options:
start-token: SEQ
end-token: END
maxseqlen: 10000
--
msu-object:
obj-name: Enter search title
obj-info: This string will be used as the Subject of the return mail
obj-tag: TITLE
obj-class: String
maxlen: 60
--
msu-object:
obj-name: Value of PAM matrix
obj-info: The amino acid weight matrix used to score non-identical amino acid pairs.
obj-tag: PAM
obj-class: Int
min: 1
max: 500
def: 120
--
msu-object:
obj-name: Enter gap penalty
obj-info: Score for gaps in alignment
obj-tag: INDEL
obj-class: Int
min: 5
max: 30
--
msu-object:
obj-name: Enter number of best alignments
obj-info: Number of alignments to show
obj-tag: ALIGN
obj-class: Int
min: 1
max: 100
def: 30
--
msu-object:
obj-name: Enter number of scores
obj-info: Number of scores to report
obj-tag: NAMES
obj-class: Int
min: 1
max: 100
def: 30
// no nuc options
###
# Weizmann BIOCCELERATOR
# 4-Mar-1994
###
service-name: BIOCCELERATOR
service-info: BIOCCELERATOR installed at Weizmann Institute of Science, Israel
service-addr: bicserv at sgbcd.weizmann.ac.il
--
help-address: bicserv at sgbcd.weizmann.ac.il
help-body: help
//
service-nuc-options:
start-token: ..
end-token: end
seq-format: ascii
lowercase: no
maxseqlen: 10000
--
msu-object:
obj-name: Select SW search
obj-tag: Bic_sw
obj-mandatory: y
obj-class: Fixed
--
msu-object:
obj-name: Show alignments
obj-info: Include alignments in output
obj-tag: align
obj-class: Boolean
def: y
--
msu-object:
obj-name: Label your sequence
obj-info: Assign a (short) name to your sequence
obj-tag: begin
obj-class: String
def: Untitled
//
service-prot-options:
start-token: ..
end-token: end
seq-format: ascii
lowercase: no
maxseqlen: 10000
--
msu-object:
obj-name: Select database
obj-info: Subset of database to be searched
obj-tag: Bic_sw
obj-mandatory: y
obj-class: Group
elements: 2
def: 1
items: -Infile2=SWISS:\*, -Infile2=PIR:\*
--
msu-object:
obj-name: Show alignments
obj-info: Include alignments in output
obj-tag: align
obj-class: Boolean
def: y
--
msu-object:
obj-name: Label your sequence
obj-info: Assign a (short) name to your sequence
obj-tag: begin
obj-class: String
def: Untitled
###
# FLASH
# 5-Oct-1993
###
service-name: FLASH
service-info: Ultra-fast seq. comparisons. Registr. req. at dflash at watson.ibm.com
service-addr: dflash at watson.ibm.com
service-subject: dflash
--
help-address: dflash at watson.ibm.com
help-subject: dflash
help-body: send help
--
reg-address: dflash at watson.ibm.com
reg-subject: Registration
reg-options:
msu-object:
obj-name: Your name
obj-tag: Name:
obj-mandatory: y
obj-class: String
msu-object:
obj-name: Your affiliation
obj-tag: Affiliation:
obj-mandatory: y
obj-class: String
msu-object:
obj-name: Your postal address
obj-tag: Address:
obj-mandatory: y
obj-class: String
msu-object:
obj-name: Your email address
obj-tag: Email:
obj-mandatory: y
obj-class: String
msu-object:
obj-name: Your phone number
obj-tag: Phone:
obj-mandatory: y
obj-class: String
//
service-prot-options:
start-token: BEGIN
end-token: 1
seq-format: fasta
minseqlen: 30
maxseqlen: 1000
--
msu-object:
obj-name: Enter PAM scoring matrix or leave blank and select BLOSUM matrix on next
question
obj-info: A value between 10 and 500 in multiples of ten. Higher values are optimal for
more distantly related sequences; lower values are better for more similar
sequences. 120 or 250 are good default values.
obj-tag: PAM
obj-class: Int
min: 10
max: 500
--
msu-object:
obj-name: Enter BLOSUM scoring matrix or leave blank if you entered a value for PAM matrix
obj-info: A value out of 30,35,40,45,50,55,60,62,65,70,75,80,85,90, or 100. Higher values
are better for more closely related sequences; lower values are better for
detecting distant sequence similarity. 62 is a good default.
obj-tag: BLOSUM
obj-class: Int
min: 30
max: 100
--
msu-object:
obj-name: Enter number of best alignments
obj-info: Number of alignments to show
obj-tag: ALIGNMENTS
obj-class: Int
min: 1
max: 10000
def: 10000
--
msu-object:
obj-name: Enter minimum score to report (threshold)
obj-info: Only scores higher than the threshold are reported
obj-tag: THRESHOLD
obj-class: Int
min: 30
max: 100
def: 50
###
# BioSCAN
# 4-May-1994
###
service-name: BioSCAN
service-info: Fast seq. comparisons using special-purpose hardware.
service-addr: bioscan at cs.unc.edu
--
help-address: bioscan at cs.unc.edu
help-body: help
//
service-nuc-options:
start-token: BEGIN
seq-format: fasta
--
msu-object:
obj-name: Program name
obj-tag: PROGRAM bscan
obj-mandatory: y
obj-class: Fixed
--
msu-object:
obj-name: Select database
obj-info: Subset of database to be searched
obj-tag: DATALIB
obj-mandatory: y
obj-class: Group
elements: 15
def: 1
items: gb,gbbct,gbest,gbinv,gbmam,gbpat,gbphg,gbpln,gbpri,gbrna,
gbrod,gbsyn,gbuna,gbvrl,gbvrt
--
msu-object:
obj-name: Report format
obj-info: Specifies the format in which results will be delivered
obj-tag: REPORT
obj-class: Group
elements: 5
def: 1
items: Segment,Simple,Align,Compress,None
--
msu-object:
obj-name: Statistical expectation
obj-info: Cutoff score for reporting hits is calculated from this value
obj-tag: EXPECT
obj-class: Float
min: 0.0001
max: 1000
def: 200
--
msu-object:
obj-name: Substitution scoring matrix
obj-info: Weight matrix for non-identical residue matches
obj-tag: MATRIX
obj-class: Group
elements: 2
def: 1
items: DPAM47I,BLOSUMN
//
service-prot-options:
start-token: BEGIN
seq-format: fasta
--
msu-object:
obj-name: Program name
obj-tag: PROGRAM bscan
obj-mandatory: y
obj-class: Fixed
--
msu-object:
obj-name: Select database
obj-info: Subset of database to be searched
obj-tag: DATALIB
obj-mandatory: y
obj-class: Group
elements: 2
def: 1
items: sw,pir
--
msu-object:
obj-name: Report format
obj-info: Specifies the format in which results will be delivered
obj-tag: REPORT
obj-class: Group
elements: 5
def: 1
items: Segment,Simple,Align,Compress,None
--
msu-object:
obj-name: Statistical expectation
obj-info: Cutoff score for reporting hits is calculated from this value
obj-tag: EXPECT
obj-class: Float
min: 0.0001
max: 1000
def: 200
--
msu-object:
obj-name: Substitution scoring matrix
obj-info: Weight matrix for non-identical residue matches
obj-tag: MATRIX
obj-class: Group
elements: 21
def: 4
items: PAM5,PAM30,PAM70,PAM120,PAM160,PAM180,PAM250,BLOSUM30,BLOSUM35,
BLOSUM40,BLOSUM45,BLOSUM50,BLOSUM55,BLOSUM62,BLOSUM70,BLOSUM75,
BLOSUM80,BLOSUM85,BLOSUM90,BLOSUM95,BLOSUM100
--
msu-object:
obj-name: Apply filter
obj-info: Eliminates biologically uninteresting reports
obj-tag: FILTER
obj-class: Boolean
def: y
###
# NCBI BLAST
# 7-Oct-1993
###
service-name: NCBI BLAST
service-info: BLAST similarity searches at the National Libr. of Medicine
service-addr: blast at ncbi.nlm.nih.gov
--
help-address: blast at ncbi.nlm.nih.gov
help-body: help
//
service-nuc-options:
start-token: BEGIN
seq-format: fasta
--
msu-object:
obj-name: Select program to use
obj-info: blastn is nucleotide seq vs. nucleotide db,
blastx is translated nucleotide seq vs. protein db
obj-tag: PROGRAM
obj-mandatory: y
obj-class: Group
elements: 2
def: 1
items: blastn,blastx
--
msu-object:
obj-name: Select database
obj-info: Subset of database to be searched
obj-tag: DATALIB
obj-mandatory: y
obj-class: Group
elements: 18
def: 1
items: nr, genbank, gbupdate, embl, emblu, pdb, vector,kabatnuc,
dbest, epd, swissprot,pir,spupdate,genpept,gpupdate,kabatpro,
tfd,palu
--
msu-object:
obj-name: Show histogram
obj-info: Displays histogram of scores
obj-tag: HISTOGRAM
obj-class: Group
elements: 2
def: 1
items: yes,no
--
msu-object:
obj-name: Enter number of scores (descriptions)
obj-info: Number of scores to report
obj-tag: DESCRIPTIONS
obj-class: Int
min: 1
max: 1000
def: 100
--
msu-object:
obj-name: Enter number of high-scoring segment pairs (alignments)
obj-info: Number of high-scoring segment pairs to report
obj-tag: ALIGNMENTS
obj-class: Int
min: 1
max: 1000
def: 50
--
msu-object:
obj-name: Scoring matrix for BLASTX (LEAVE BLANK FOR BLASTN searches!)
obj-tag: MATRIX
obj-class: Group
elements: 4
items: BLOSUM62,PAM40,PAM120,PAM250
--
msu-object:
obj-name: Return email address
obj-info: An alternative email address to which results should be sent
obj-tag: PATH
obj-class: String
//
service-prot-options:
start-token: BEGIN
seq-format: fasta
--
msu-object:
obj-name: Select program to use
obj-info: blastp is protein seq vs. protein db,
tblastn is protein seq vs. translated nucleotide db
obj-tag: PROGRAM
obj-mandatory: y
obj-class: Group
elements: 2
def: 1
items: blastp, tblastn
--
msu-object:
obj-name: Select database
obj-info: Subset of database to be searched
obj-tag: DATALIB
obj-mandatory: y
obj-class: Group
elements: 18
def: 1
items: nr,swissprot,pir,spupdate,genpept,gpupdate,pdb,kabatpro,
tfd,palu, genbank, gbupdate, embl, emblu, pdb, vector,kabatnuc,
dbest, epd
--
msu-object:
obj-name: Show histogram
obj-info: Displays histogram of scores
obj-tag: HISTOGRAM
obj-class: Group
elements: 2
def: 1
items: yes,no
--
msu-object:
obj-name: Enter number of scores (descriptions)
obj-info: Number of scores to report
obj-tag: DESCRIPTIONS
obj-class: Int
min: 1
max: 1000
def: 100
--
msu-object:
obj-name: Enter number of high-scoring segment pairs (alignments)
obj-info: Number of high-scoring segment pairs to report
obj-tag: ALIGNMENTS
obj-class: Int
min: 1
max: 1000
def: 50
--
msu-object:
obj-name: Scoring matrix applied for sequence comparisons
obj-tag: MATRIX
obj-class: Group
elements: 4
items: BLOSUM62,PAM40,PAM120,PAM250
--
msu-object:
obj-name: Apply filter
obj-info: Eliminates biologically uninteresting reports
obj-tag: FILTER
obj-class: Boolean
def: y
--
msu-object:
obj-name: Return email address
obj-info: An alternative email address to which results should be sent
obj-tag: PATH
obj-class: String
####
# EMBL FASTA server
# 4-Oct-1993
###
service-name: EMBL FASTA server
service-info: Protein and nucleotide database searches using the FASTA algorithm
service-addr: fasta at embl-heidelberg.de
--
help-address: fasta at embl-heidelberg.de
help-body: help
//
service-nuc-options:
start-token: SEQ
end-token: END
maxseqlen: 32000
--
msu-object:
obj-name: Select database
obj-info: Subset of database to be searched
obj-tag: LIB
obj-class: Group
elements: 20
def: 1
items: EMALL,EMNEW,EFUN,EINV,EMAM,EORG,EPHG,EPLN,EPRI,EPRO,EROD,ESYN,EUNA,EVRL,
EVRT,GBNEW,GBALL,GBONLY, GENEMBL, GENEW
--
msu-object:
obj-name: Enter k-tupel value (word size)
obj-info: Controls the sensitivity of search. The lower the case the more sensitive
the search, but also the longer the execution time
obj-tag: WORD
obj-class: Int
min: 3
max: 6
def: 6
--
msu-object:
obj-name: Enter number of scores
obj-info: Number of scores to report
obj-tag: LIST
obj-class: Int
min: 1
max: 100
def: 50
--
msu-object:
obj-name: Enter number of best alignments
obj-info: Number of alignments to report
obj-tag: ALIGN
obj-class: Int
min: 1
max: 30
def: 10
--
msu-object:
obj-name: Search one strand only
obj-info: Search one strand only. By default, both strands will be searched
obj-tag: ONE
obj-class: Boolean
def: no
--
msu-object:
obj-name: Enter search title
obj-info: This string will be used as the Subject of the return mail
obj-tag: TITLE
obj-class: String
maxlen: 60
//
service-prot-options:
start-token: SEQ
end-token: END
maxseqlen: 32000
--
msu-object:
obj-name: Select database
obj-info: Subset of database to be searched
obj-tag: LIB
obj-class: Group
elements: 8
def: 1
items: SWALL, SWNEW, SW, NBRF, PIRONLY, SWISSPIRALL, BROOKHAVEN, NRL
--
msu-object:
obj-name: Enter k-tupel value (word size)
obj-info: Controls the sensitivity of search. The lower the case the more sensitive
the search, but also the longer the execution time
obj-tag: WORD
obj-class: Int
min: 1
max: 2
def: 2
--
msu-object:
obj-name: Enter number of scores
obj-info: Number of scores to report
obj-tag: LIST
obj-class: Int
min: 1
max: 100
def: 50
--
msu-object:
obj-name: Enter number of best alignments
obj-info: Number of alignments to report
obj-tag: ALIGN
obj-class: Int
min: 1
max: 30
def: 10
--
msu-object:
obj-name: Enter search title
obj-info: This string will be used as the Subject of the return mail
obj-tag: TITLE
obj-class: String
maxlen: 60
####
# PIR FASTA server
# 6-Oct-1993
###
service-name: NBRF/PIR FASTA server
service-info: Protein database searches using the FASTA algorithm
service-addr: fileserv at nbrf.georgetown.edu
--
help-address: fileserv at nbrf.georgetown.edu
help-body: help search
//
service-nuc-options:
seq-format: pir
end-token: END SEARCH
--
msu-object:
obj-name: Enter k-tupel value (word size)
obj-info: Controls the sensitivity of search. The lower the case the more sensitive
the search, but also the longer the execution time
obj-tag: SEARCH KTUP=
obj-class: Int
min: 3
max: 6
def: 6
//
service-prot-options:
seq-format: pir
end-token: END SEARCH
--
msu-object:
obj-name: Enter k-tupel value (word size)
obj-info: Controls the sensitivity of search. The lower the case the more sensitive
the search, but also the longer the execution time
obj-tag: SEARCH KTUP=
obj-class: Int
min: 1
max: 2
def: 2
###
# EMBL QuickSearch
# 4-Oct-1993
###
service-name: EMBL QuickSearch server
service-info: Rapid comparisons of nucleotide sequences, looking for close matches.
service-addr: quick at EMBL-Heidelberg.DE
--
help-address: quick at EMBL-Heidelberg.DE
help-body: help
//
service-nuc-options:
start-token: SEQ
end-token: END
maxseqlen: 100000
--
msu-object:
obj-name: Select sequence library
obj-info: Subset of database to be searched
obj-tag: LIB
obj-class: Group
elements: 2
def: 1
items: ALL,GENEW
--
msu-object:
obj-name: Enter window size
obj-info: Decreasing the window size will increase the sensitivity of the comparison.
Leave blank if you don't know what you are doing
obj-tag: WINDOW
obj-class: Int
min: 1
max: 50
--
msu-object:
obj-name: Enter stringency
obj-info: Decreasing the window size will increase the sensitivity of the comparison.
Leave blank if you don't know what you are doing
obj-tag: STRINGENCY
obj-class: Int
min: 1
max: 50
--
msu-object:
obj-name: Set Perfect flag
obj-info: Only perfect matches will be found
obj-tag: PERFECT
obj-class: Boolean
def: no
--
msu-object:
obj-name: Enter minimum percentage of matches
obj-info: Only hits with overlaps of more than n% identity will be presented
obj-tag: MATCH
obj-class: Int
min: 0
max: 100
def: 90
--
msu-object:
obj-name: Use local homology alignment
obj-info: If set to yes, a local homology algorithm will be used.
By default, a Needleman-Wunsch alignment is created
obj-tag: BEST
obj-class: Boolean
def: no
--
msu-object:
obj-name: Search one strand only
obj-info: Search one strand only. By default, both strands will be searched
obj-tag: ONE
obj-class: Boolean
def: no
--
msu-object:
obj-name: Enter title of sequence
obj-info: Short description of the sequence. Will be used as the Subject line
of the reply
obj-tag: TITLE
obj-class: String
maxlen: 70
// no prot options
###
# CBRG (ETH Zuerich)
###
service-name: CBRG (ETH Zuerich)
service-info: Exhaustive search of SWISS-PROT protein sequence database
service-addr: cbrg at inf.ethz.ch
--
help-address: cbrg at inf.ethz.ch
help-subject: help
help-body: help
//
service-nuc-options:
start-token: NuclPepSearch
lowercase: no
--
service-prot-options:
start-token: PepPepSearch
lowercase: no
###
# BLOCKS server
# 4-Oct-1993
###
service-name: BLOCKS server
service-info: Comparison of protein or DNA sequences against database of protein blocks
service-addr: blocks at howard.fhcrc.org
--
help-address: blocks at howard.fhcrc.org
help-body: help
//
service-prot-options:
seq-format: fasta
//
service-nuc-options:
seq-format: fasta
###
# Mail-PROSITE
# 26-Apr-1994
###
service-name: EMBL PROSITE server
service-info: Pattern searches using PROSITE database
service-addr: prosite at embl-heidelberg.de
--
help-address: prosite at embl-heidelberg.de
help-body: help
//
service-prot-options:
start-token: SEQ
seq-format: ascii
end-token: END
--
msu-object:
obj-name: Enter search title
obj-info: This string will be used as the Subject of the return mail
obj-tag: TITLE
obj-class: String
maxlen: 60
---
msu-object:
obj-name: Include abundant patterns in search
obj-info: Include abundant patterns. By default, they are excluded.
obj-tag: FULL
obj-class: Boolean
def: no
// no nuc options
###
# MotifFinder
###
service-name: MotifFinder
service-info: Motif finding tool at genome.ad.jp
service-addr: motif at genome.ad.jp
--
help-address: motif at genome.ad.jp
help-body: help
//
service-prot-options:
seq-format: fasta
--
msu-object:
obj-name: Select motif library
obj-info: The motif library to be searched
obj-tag: DATALIB
obj-class: group
elements: 2
def: 1
items: Prosite,MotifDic
// no nuc options
###
# ProteinPredict
# 4-Oct-1993
###
service-name: ProteinPredict
service-info: Neural network secondary protein structure prediction
service-addr: PredictProtein at embl-heidelberg.de
--
help-address: PredictProtein at embl-heidelberg.de
help-subject: help
//
service-prot-options:
--
msu-object:
obj-name: Your name
obj-info: Enter your full name here
obj-tag: name:
obj-mandatory: y
obj-class: string
maxlen: 60
--
msu-object:
obj-name: Your address (part1)
obj-info: Enter your postal address here
obj-tag: address1:
obj-mandatory: y
obj-class: string
maxlen: 60
--
msu-object:
obj-name: Your address (part2)
obj-info: Enter your postal address here
obj-tag: address2:
obj-mandatory: n
obj-class: string
maxlen: 60
--
msu-object:
obj-name: Your email address
obj-info: Enter your email address here
obj-tag: email:
obj-mandatory: y
obj-class: string
maxlen: 60
--
msu-object:
obj-name: Enter sequence description
obj-info: A brief description of the sequence
obj-tag: #
obj-mandatory: y
obj-class: string
maxlen: 78
// no nuc options
###
# nnpredict
# 4-Oct-1993
###
service-name: nnpredict
service-info: Neural network secondary protein structure prediction
service-addr: nnpredict at celeste.ucsf.edu
--
help-address: nnpredict at celeste.ucsf.edu
help-subject: help
help-body: help
//
service-prot-options:
lowercase: n
seq-format: fasta
--
msu-object:
obj-name: Select prediction options
obj-info: nnpredict uses the secondary structure class for prediction:
(n) use no tertiary structure class for prediction (the default)
(a) use all-alpha tertiary structure class for prediction
(b) use all-beta tertiary structure class for prediction
(a/b) use alpha/beta tertiary structure class for prediction
obj-tag: option:
obj-class: Group
elements: 4
def: 1
items: n,a,b,a/b
// no nuc options
###
# NetGene
# 4-Oct-1993
###
service-name: NetGene
service-info: Neural network prediction of splice sites in vertebrates
service-addr: netgene at virus.fki.dth.dk
--
help-address: netgene at virus.fki.dth.dk
help-subject: help
help-body: help
//
service-nuc-options:
seq-format: fasta
minseqlen: 451
maxseqlen: 100000
// no prot options
###
# Grail
# 4-Oct-1993
###
service-name: Grail
service-info: Gene finding service. Registration required at grail at ornl.gov
service-addr: grail at ornl.gov
--
help-address: grail at ornl.gov
help-body: help
--
reg-address: grail at ornl.gov
reg-subject: Registration
reg-options:
msu-object:
obj-name: Your name
obj-tag: Name:
obj-mandatory: y
obj-class: String
msu-object:
obj-name: Your affiliation
obj-tag: Affiliation:
obj-mandatory: y
obj-class: String
msu-object:
obj-name: Your postal address
obj-tag: Address:
obj-mandatory: y
obj-class: String
msu-object:
obj-name: Your email address
obj-tag: Email:
obj-mandatory: y
obj-class: String
msu-object:
obj-name: Your phone number
obj-tag: Phone:
obj-mandatory: y
obj-class: String
//
service-nuc-options:
seq-format: fasta
minseqlen: 100
maxseqlen: 100000
--
msu-object:
obj-name: Your GRAIL user ID
obj-info: Enter the user id you received when registering with GRAIL
obj-tag: Sequences 1
obj-class: String
// no prot options
###
# GeneID
# 4-Oct-1993
###
service-name: GeneID (less than 20kb)
service-info: Pediction of exons and gene structure.
service-addr: geneid at darwin.bu.edu
--
help-address: geneid at darwin.bu.edu
help-body: help
//
service-nuc-options:
start-token: Genomic Sequences
seq-format: fasta
minseqlen: 100
maxseqlen: 20000
--
msu-object:
obj-name: Suppress automatic comparison of best model with protein database
obj-info: The top-ranking model will NOT be submitted to NCBI's BLAST server
obj-tag: Genomic Sequence -noblast
obj-class: Boolean
def: no
// no prot options
###
# GenMark
# 4-Oct-1993
###
service-name: GenMark
service-info: Gene finding service. Registration required at genmark at ford.gatech.edu
service-addr: genmark at ford.gatech.edu
service-subject: genmark
--
help-address: genmark at ford.gatech.edu
help-subject: instructions
--
reg-address: genmark at ford.gatech.edu
reg-subject: Registration
reg-options:
msu-object:
obj-name: Your name
obj-tag: Name:
obj-mandatory: y
obj-class: String
msu-object:
obj-name: Your affiliation
obj-tag: Affiliation:
obj-mandatory: y
obj-class: String
msu-object:
obj-name: Your postal address
obj-tag: Address:
obj-mandatory: y
obj-class: String
msu-object:
obj-name: Your email address
obj-tag: Email:
obj-mandatory: y
obj-class: String
msu-object:
obj-name: Your phone number
obj-tag: Phone:
obj-mandatory: y
obj-class: String
//
service-nuc-options:
start-token: data
--
msu-object:
obj-name: Select species matrix
obj-info: Matrix used to analyze submitted sequence
obj-tag: SPECIES
obj-class: Group
elements: 4
def: 1
items: ecoli, hiexpress,ecophage, human
--
msu-object:
obj-name: Enter title of analysis
obj-info: Short description of the sequence. Will be used as identifier in the reply.
obj-tag: TITLE
obj-class: String
--
msu-object:
obj-name: Select graphical output (PostScript file)
obj-info: Will deliver results in the form of a Postscript File
obj-tag: PSGRAPH
obj-class: Boolean
def: n
--
msu-object:
obj-name: Return CDS predictions with regions
obj-info: GenMark replies with a list of regions containing possible coding regions
from stop codon to stop codon
obj-tag: PROTEIN region
obj-class: Boolean
def: n
--
msu-object:
obj-name: Return CDS predictions with ORFs
obj-info: GenMark replies with a list of open reading frames (splice site to splice
site)
obj-tag: PROTEIN orf
obj-class: Boolean
def: n
--
msu-object:
obj-name: Send predicted ORFs automatically to BLAST server
obj-info: ORFs in which coding regions are predicted are automatically submitted to
NCBI's BLAST server for homology searches
obj-tag: PROTEIN send
obj-class: Boolean
def: n
--
msu-object:
obj-name: Send nucleotide sequences of predicted ORFs automatically to BLAST server
obj-info: Nucleotide sequences of ORFs in which coding regions are predicted are
automatically submitted to NCBI's BLAST server for homology searches
obj-tag: NUCSEQ send
obj-class: Boolean
def: n
--
msu-object:
obj-name: Select ORF list display format
obj-info: orf gives detailed assessment of regions between splice-sites that are
predicted to contain coding regions;
region cites regions from stop codon to stop codon in which a coding region
was predicted;
off tells GenMark not to reply with an ORF list
obj-tag: ORFLIST
obj-class: Group
elements: 3
def: 1
items: orf, region, off
--
msu-object:
obj-name: Enter alternative email address
obj-info: Fill in if GenMark should use alternative email address
obj-tag: ADDRESS
obj-class: String
--
msu-object:
obj-name: Enter user name
obj-info: You may fill in your name here for identification purposes
obj-tag: NAME
obj-class: String
--
msu-object:
obj-name: Enter Markov chain order
obj-info: Specifies the order of the Markov chain used to analyze the sequence.
Should be unnecessary to specify
obj-tag: ORDER
obj-class: Int
/* Don't know whether these values have any resemblance to reality */
min: 1
max: 10
--
msu-object:
obj-name: Enter window size
obj-info: Length of the analysis window that the GenMark algorithm uses. Smaller values
will produce a higher rate of false signals, but may show smaller coding
regions. Larger values will clarify the signal of larger regions but yield
lower sensitivity. Should be unnecessary to modify
obj-tag: WINDOW
obj-class: Int
min: 1
max: 100000
def: 96
--
msu-object:
obj-name: Enter window step size
obj-info: Step size that the GenMark algorithm uses to advance the window. Smaller values
increase the resolution of a graph and increases the output size.
Should be unnecessary to modify
obj-tag: STEP
obj-class: Int
min: 1
max: 100000
def: 12
--
msu-object:
obj-name: Enter prediction threshold
obj-info: This threshold will be used to judge whether a region should be predicted as
coding
obj-tag: THRESHOLD
obj-class: Float
min: 0
max: 1
def: 0.6
// no prot options
###
# Pythia
# 4-Oct-1993
###
service-name: PYTHIA (Rpts)
service-info: Identification of occurrences of repetitive DNA elements
service-addr: pythia at anl.gov
service-subject: Rpts
--
help-address: pythia at anl.gov
help-subject: help
//
service-nuc-options:
seq-format: ig
maxseqlen: 10000
lowercase: no
//
service-name: PYTHIA (Alu)
service-info: Identification of subfamily membership of Alu sequences
service-addr: pythia at anl.gov
service-subject: Alu
--
help-address: pythia at anl.gov
help-subject: help
//
service-nuc-options:
seq-format: ig
maxseqlen: 10000
lowercase: no
###
# GenomeNet BLAST
# 5-Oct-1993
###
service-name: GenomeNet BLAST
service-info: BLAST similarity searches on the Japanese GenomeNet server
service-addr: blast at genome.ad.jp
--
help-address: blast at genome.ad.jp
help-body: help
//
service-nuc-options:
start-token: BEGIN
seq-format: fasta
--
msu-object:
obj-name: Select program to use
obj-info: blastn is nucleotide seq vs. nucleotide db,
blastx is translated nucleotide seq vs. protein db
obj-tag: PROGRAM
obj-mandatory: y
obj-class: Group
elements: 2
def: 1
items: blastn,blastx
--
msu-object:
obj-name: Select database
obj-info: Subset of database to be searched
obj-tag: DATALIB
obj-mandatory: y
obj-class: Group
elements: 7
def: 1
items: nr-nt, genbank, embl,nr-aa, swissprot, pir,prf
--
msu-object:
obj-name: Enter number of scores
obj-info: Number of scores to report
obj-tag: V=
obj-class: Int
min: 1
max: 1000
def: 500
--
msu-object:
obj-name: Enter number of high-scoring segment pairs
obj-info: Number of high-scoring segment pairs to report
obj-tag: B=
obj-class: Int
min: 1
max: 1000
def: 250
--
msu-object:
obj-name: Enter score for matches
obj-info: The score to assign to a single-letter match
obj-tag: M=
obj-class: Int
min: 1
max: 1000
def: 5
--
msu-object:
obj-name: Enter score for mismatches
obj-info: The score to assign to a single-letter mismatch
obj-tag: N=
obj-class: Int
min: -1000
max: -1
def: -4
//
service-prot-options:
start-token: BEGIN
seq-format: fasta
--
msu-object:
obj-name: Select program to use
obj-info: blastp is protein seq vs. protein,
tblastn is protein seq vs. translated nucleotide db
obj-tag: PROGRAM
obj-class: Group
elements: 2
def: 1
items: blastp,tblastn
--
msu-object:
obj-name: Select database
obj-info: Subset of database to be searched
obj-tag: DATALIB
obj-mandatory: y
obj-class: Group
elements: 7
def: 1
items: nr-aa, swissprot,pir,prf,pdbstr, nr-nt, genbank,embl
--
msu-object:
obj-name: Enter number of scores
obj-info: Maximum number of scores to report
obj-tag: V=
obj-class: Int
min: 1
max: 1000
def: 500
--
msu-object:
obj-name: Enter number of high-scoring segment pairs
obj-info: Maximum number of high-scoring segment pairs to report
obj-tag: B=
obj-class: Int
min: 1
max: 1000
def: 250
###
# GenomeNet FASTA
# 5-Oct-1993
###
service-name: GenomeNet FASTA
service-info: FASTA similarity searches on the Japanese GenomeNet server
service-addr: fasta at genome.ad.jp
--
help-address: fasta at genome.ad.jp
help-body: help
//
service-nuc-options:
start-token: BEGIN
seq-format: fasta
--
msu-object:
obj-name: Select database
obj-info: Subset of database to be searched
obj-tag: DATALIB
obj-mandatory: y
obj-class: Group
elements: 30
def: 1
items: nr-nt, genbank,genbank-upd, genbank/primate,genbank/rodent,
genbank/other_mammalian,genbank/other_vertebrate,genbank/invertebrate,
genbank/plant,genbank/bacterial,genbank/structural_rna,
genbank/viral,genbank/phage,genbank/synthetic,genbank/unannotated,
genbank/est,genbank/patent, embl,embl/bacteriophage,embl/fungi,
embl/invertebrate,embl/organelle,embl/other_mammalian,
embl/other_vertebrate,embl/plant,embl/primate,embl/prokaryote,
embl/rodent,embl/synthetic,embl/unannotated,embl/viral
--
msu-object:
obj-name: Enter k-tupel value (word size)
obj-info: Controls the sensitivity of search. The lower the case the more sensitive
the search, but also the longer the execution time
obj-tag: KTUP
obj-class: Int
min: 3
max: 6
def: 6
--
msu-object:
obj-name: Enter number of scores
obj-info: Number of scores to report
obj-tag: -b
obj-class: Int
min: 1
max: 100
def: 50
--
msu-object:
obj-name: Enter number of best alignments
obj-info: Number of alignments to report
obj-tag: -d
obj-class: Int
min: 1
max: 100
def: 10
//
service-prot-options:
start-token: BEGIN
seq-format: fasta
--
msu-object:
obj-name: Select program to use
obj-info: FASTA is protein seq vs. protein db,
TFASTA is protein seq vs. translated nucleotide db
obj-tag: PROGRAM
obj-class: Group
elements: 2
def: 1
items: fasta,tfasta
--
msu-object:
obj-name: Select database
obj-info: Subset of database to be searched
obj-tag: DATALIB
obj-mandatory: y
obj-class: Group
elements: 35
def: 1
items: nr-aa, swissprot,pir,prf,pdbstr,
nr-nt, genbank,genbank-upd, genbank/primate,genbank/rodent,
genbank/other_mammalian,genbank/other_vertebrate,genbank/invertebrate,
genbank/plant,genbank/bacterial,genbank/structural_rna,
genbank/viral,genbank/phage,genbank/synthetic,genbank/unannotated,
genbank/est,genbank/patent, embl,embl/bacteriophage,embl/fungi,
embl/invertebrate,embl/organelle,embl/other_mammalian,
embl/other_vertebrate,embl/plant,embl/primate,embl/prokaryote,
embl/rodent,embl/synthetic,embl/unannotated,embl/viral
--
msu-object:
obj-name: Enter k-tupel value (word size)
obj-info: Controls the sensitivity of search. The lower the case the more sensitive
the search, but also the longer the execution time
obj-tag: KTUP
obj-class: Int
min: 1
max: 2
def: 2
--
msu-object:
obj-name: Enter number of scores
obj-info: Number of scores to report
obj-tag: -b
obj-class: Int
min: 1
max: 100
def: 50
--
msu-object:
obj-name: Enter number of best alignments
obj-info: Number of alignments to report
obj-tag: -d
obj-class: Int
min: 1
max: 100
def: 10
###
# GenQuest (Q)
# 1-Nov-1993
###
service-name: GenQuest (Q)
service-info: Database searches
service-addr: q at ornl.gov
--
help-address: q at ornl.gov
help-body: help
//
service-nuc-options:
start-token: SEQ
end-token: END
seq-format: ascii
--
msu-object:
obj-name: Sequence type
obj-tag: TYPE DNA
obj-mandatory: y
obj-class: Fixed
--
msu-object:
obj-name: Select database
obj-info: Database to be searched
obj-tag: TARGET
obj-class: Group
elements: 2
def: 1
items: GSDB, Repetitive
--
msu-object:
obj-name: Select search method
obj-info: Search method to be used (SW = Smith-Waterman)
obj-tag: METHOD
obj-class: Group
elements: 4
def: 1
items: SW, FASTA, BLAST, FLASH
--
msu-object:
obj-name: Apply filter for repetitive sequences
obj-info: Removes repetitive elements from query sequence
obj-tag: FILTER
obj-class: Boolean
def: y
--
msu-object:
obj-name: Enter comment
obj-info: To tag your sequence with some identifier
obj-tag: COMMENT
obj-class: String
--
msu-object:
obj-name: Enter number of scores (only for SW searches)
obj-info: Number of scores to report
obj-tag: SCORE
obj-class: Int
min: 1
max: 1000
def: 10
--
msu-object:
obj-name: Enter number of alignments (only for SW searches)
obj-info: Number of alignments to report
obj-tag: ALIGN
obj-class: Int
min: 1
max: 1000
def: 10
//
service-prot-options:
start-token: SEQ
end-token: END
seq-format: ascii
--
msu-object:
obj-name: Sequence type
obj-tag: TYPE PROTEIN
obj-mandatory: y
obj-class: Fixed
--
msu-object:
obj-name: Select database
obj-info: Database to be searched
obj-tag: TARGET
obj-class: Group
elements: 3
def: 1
items: SWISSPROT, PDB, PROSITE
--
msu-object:
obj-name: Select search method
obj-info: Search method to be used (SW = Smith-Waterman)
obj-tag: METHOD
obj-class: Group
elements: 4
def: 1
items: SW, FASTA, BLAST, FLASH
--
msu-object:
obj-name: Scoring matrix
obj-info: Scoring matrix applied for sequence comparisons
obj-tag: MATRIX
obj-class: Group
elements: 5
def: 1
items: BLOSUM60, BLOSUM80, PAM40, PAM120, PAM250
--
msu-object:
obj-name: Enter comment
obj-info: To tag your sequence with some identifier
obj-tag: COMMENT
obj-class: String
--
msu-object:
obj-name: Enter number of scores (only for SW searches)
obj-info: Number of scores to report
obj-tag: SCORE
obj-class: Int
min: 1
max: 1000
def: 10
--
msu-object:
obj-name: Enter number of alignments (only for SW searches)
obj-info: Number of alignments to report
obj-tag: ALIGN
obj-class: Int
min: 1
max: 1000
def: 10
###
# SBASE Mail server
# 10-Dec-1993
###
service-name: SBASE
service-info: Protein domain detection
service-addr: sbase at icgeb.trieste.it
--
help-address: sbase at icgeb.trieste.it
help-body: help
//
service-prot-options:
start-token: BEGIN
seq-format: FASTA
--
msu-object:
obj-name: Include annotation
obj-info: Include complete annotation of domains in output
obj-tag: ANNOTATIONS
obj-class: Group
elements: 2
def: 1
items: YES, NO
--
msu-object:
obj-name: Scoring matrix
obj-info: Scoring matrix applied for sequence comparisons
obj-tag: MATRIX
obj-class: Group
elements: 5
def: 1
items: PAM120, PAM250, PAM40, BLOSUM60, BLOSUM80
--
msu-object:
obj-name: Cutoff score
obj-info: Cutoff score for displaying homologies
obj-tag: SCORE PARAMETER
obj-class: Int
min: 30
max: 100
def: 35
###
# ProDom
# 14-Mar-1994
###
service-name: ProDom
service-info: ProDom domain searches
service-addr: prodom at toulouse.inra.fr
--
help-address: prodom at toulouse.inra.fr
help-body: help
//
service-nuc-options:
start-token: BEGIN
end-token: END
seq-format: fasta
--
msu-object:
obj-name: Search type
obj-tag: PROGRAM blastx
obj-mandatory: y
obj-class: Fixed
//
service-prot-options:
start-token: BEGIN
end-token: END
seq-format: fasta
--
msu-object:
obj-name: Search type
obj-tag: PROGRAM blastp
obj-mandatory: y
obj-class: Fixed
###
# GCRDb
# 26-Apr-1994
###
service-name: GCRDb (G-protein coupled receptors)
service-info: FASTA searches of G-protein-coupled receptor database
service-addr: gcrdb at receptor.mgh.harvard.edu
--
help-address: gcrdb at receptor.mgh.harvard.edu
help-body: help
//
service-prot-options:
seq-format: fasta
//
