A new release of the NCBI toolkit as well as BLAST 2.0.2 binaries
are now available from the NCBI FTP Site (ncbi.nlm.nih.gov). The
toolkit archive contains source code to compile BLAST 2.0.2 as well as
a small number of incremental changes in the ASN.1 specification.
Toolkit archives may be found under 'toolbox/ncbi_tools'. BLAST binaries
may be found under 'blast/executables'.
BLAST 2.0 - BLAST 2.0 can produce gapped alignments and is capable of
position-specific-iterated BLASTp (PSI-BLAST). Compared to the 1.4 release of
BLAST, there are also signficant performance enhancements as well as extensive
changes to the text report and the format of the databases. BLAST 2.0
uses threads for multi-processing, using the NCBI threads library.
Three BLAST programs may be compiled in the demo of the toolbox or obtained
from the 'blast/executables' directory. They are:
formatdb: formats FASTA files as BLAST databases for BLAST 2.0.
blastall: perform all five flavors of blast comparison. blastn and blastp offer
fully
gapped alignments. blastx and tblastn have 'in-frame' gapped alignments
and
use sum statistics to link alignments from different frames. tblastx
provides
only ungapped alignments.
blastpgp: performs gapped blastp searches and can be used to perform iterative
searches in psi-blast mode.
Additional information may be obtained from the README in the BLAST directory of
the
FTP site and from the NCBI BLAST pages.
ASN.1 Spec Changes for 1997
biblio.asn
Cit-pat - some fields made optional to allow patent applications to be legal
Cit-pat.number OPTIONAL
Cit-pat.date-issue OPTIONAL
-- Patent number and date-issue were made optional in 1997 to
-- support patent applications being issued from the USPTO
-- Semantically a Cit-pat must have either a patent number or
-- an application number (or both) to be valid
medline.asn
added ML-field to support other MEDLINE line types
added Medline-entry.status
added gdb as a valid Medline-si type
Medline-entry ::= SEQUENCE {
uid INTEGER OPTIONAL , -- MEDLINE UID, sometimes not yet available if
from PubMed
em Date , -- Entry Month
cit Cit-art , -- article citation
abstract VisibleString OPTIONAL ,
mesh SET OF Medline-mesh OPTIONAL ,
substance SET OF Medline-rn OPTIONAL ,
xref SET OF Medline-si OPTIONAL ,
idnum SET OF VisibleString OPTIONAL , -- ID Number (grants, contracts)
gene SET OF VisibleString OPTIONAL ,
pmid PubMedId OPTIONAL , -- MEDLINE records may include the
PubMedId
pub-type SET OF VisibleString OPTIONAL, -- may show publication types
(review, etc)
mlfield SET OF Medline-field OPTIONAL , -- additional Medline field types
status INTEGER {
publisher (1) , -- record as supplied by publisher
premedline (2) , -- premedline record
medline (3) } DEFAULT medline } -- regular medline record
Medline-field ::= SEQUENCE {
type INTEGER { -- Keyed type
other (0) , -- look in line code
comment (1) , -- comment line
erratum (2) } , -- retracted, corrected, etc
str VisibleString , -- the text
ids SEQUENCE OF DocRef OPTIONAL } -- pointers relevant to this text
DocRef ::= SEQUENCE { -- reference to a document
type INTEGER {
medline (1) ,
pubmed (2) ,
ncbigi (3) } ,
uid INTEGER }
seq.asn
MolInfo.tech - added names for HTG classes already implemented
Annotdesc.region - added seqloc. If present, all annots in this SeqAnnot
are within this region. Optimization on big seqs.
seqfeat.asn
added OrgMod.specimen-voucher - new organism qualifier
added OrgMod.old-name - used internally at NCBI
added BioSource.is-focus - for distinguishing biological focus of
multiple source features.
added Seq-feat.pseudo so any feature can be flagged explicitly as
belonging to a pseudogene
added Seq-feat.except-text for an explanation of the exception when
Seq-feat.except is TRUE. Currently this text is in Seq-feat.comment
in backbone records and GBQuals in some other genbank records.
