New NCBI toolkit and BLAST 2.0 release

Tom Madden madden at CORIN.NLM.NIH.GOV
Wed Sep 10 12:39:39 EST 1997

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 
	gapped alignments.  blastx and tblastn have 'in-frame' gapped alignments 
	use sum statistics to link alignments from different frames. tblastx 
	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 
FTP site and from the NCBI BLAST pages.

ASN.1 Spec Changes for 1997

  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

  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 
    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 }

  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.

  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.

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