Important announcement about SeqAnalRef

Amos Bairoch BAIROCH at
Thu Jan 14 20:32:44 EST 1993

SEQANALREF release 33 is now available
SeqAnalRef is a  bibliographic reference data bank relative  to papers dealing
with sequence analysis. The majority of entries belong to one of the following
 - Algorithms for protein and nucleic acid sequence analysis
 - Algorithms for sequence-based phylogenetic analysis.
 - Descriptions of biopolymer data banks
 - Descriptions of software packages.
 - Descriptions of on-line services for molecular biologists.
WHATS NEW ?     !!!!!! VERY IMPORTANT !!!!!!
We normally do not announce new releases of SeqAnalRef as the data base is
updated  every  other  month, but  this  release  brings  an important new
improvement. In  addition  to  the  data  file  containing  the references
(SEQANALR.DAT) [2027 references in this release],  there  is  a  new  file
(SEQANALR.ABS) containing  the full  text  of the abstracts of some of the
papers [993 in this release] referenced in SeqAnalRef.
Cross-referencing between  the  two  files  is  done  using  the Reference
identifier (on the ID line).  Example:
 |          |
 |     ID   HENS9101
 |     RM   92093619
 |     RA   Henikoff S., Henikoff J.G.;
 |     RT   "Automatic generation of protein blocks for database searching.";
 |     RL   Nucleic Acids Res. 19:6565-6572(1991).
 |     CC   Abstract.
 |     //      |
 |             |
 |             v
 |             Indicates that the abstract for this reference is available
A system  is described for finding and assembling the most highly conserved
regions of  related proteins  for database  searching. First,  an automated
version of  Smith's algorithm  for finding  motifs is  used  for  sensitive
detection of  multiple local  alignments. Next,  the local  alignments  are
converted  to  blocks  and  the  best  set  of  non-overlapping  blocks  is
determined. When  the automated  system was applied successively to all 437
groups of  related proteins  in the  PROSITE catalog, 1764 blocks resulted;
these could be used for very sensitive searches of sequence databases. Each
block was  calibrated by  searching the  SWISS-PROT database  to  obtain  a
measure of  the chance  distribution of  matches, and the calibrated blocks
were concatenated  into a  database that could itself be searched. Examples
are provided in which distant relationships are detected either using a set
of blocks  to search  a sequence  database or using sequences to search the
database  of   blocks.  The   practical  use  of  the  blocks  database  is
demonstrated  by   detecting  previously   unknown  relationships   between
oxidoreductases and  by evaluating  a proposed relationship between HIV Vif
protein and thiol proteases.
These abstracts were obtained from various  sources,  the  majority were 
extracted from the molecular subset of Medline distributed in the Entrez
CD-ROM from the NCBI. 
There are a number  of journals that do not  publish abstracts; we  hope
that  the  authors  of  papers without abstracts  that are listed in the 
database will send  us electronic copies of the full article  so that we
can produce an abstract.
If you are on Internet you can get the latest version of SeqAnalRef from
the following FTP  servers (you should always login as user = anonymous,
password: your name or email address).
    Organism : National Center for Biotechnology Information (NCBI)
    Address  : (or
    Directory: /repository/seqanalref
    Organism : EMBL
    Address  : (or
    Directory: /pub/databases/reflist
    Organism : Basel Biozentrum Biocomputing server (EMBnet SWISS node)
    Address  : (or
    Directory: /archive_data/database/references/seqanalref
    Organism : ExPASy (Geneva University Expert Protein Analysis System)
    Address  :  (or
    Directory: /databases/seqanalref
| Amos Bairoch                | Email: bairoch at                 |
| Dept. Medical Biochemistry  |    or  bairoch at cgecmu51.bitnet              |
| C.M.U.                      +---------------------------------------------+
| 1, rue Michel Servet        | Tel  : +(41 22) 361 84 92                   |
| 1211 Geneva 4               | Fax  : +(41 22) 347 33 34                   |
| Switzerland                 |                                             |

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