PIRALN database of Protein Sequence Alignments release 19.0 available

Christopher R. Marzec MARZEC at NBRF.Georgetown.Edu
Mon May 4 10:22:28 EST 1998


The PIRALN Protein Sequence Alignment Database is a database of protein
alignments produced by L.-S. Yeh, G.Y. Srinivasarao and C.R. Marzec of
NBRF/PIR. It is derived from sequences in the PIR-International Protein
Sequence Database. Alignment entries are one of three types: sequences
from one family which are less than 55% different from each other,
sequences representing various families within a superfamily or sequence
segments corresponding to some homology domain found in multiple
proteins.

Release 19.0, March 1998, of the PIRALN database contains a total of
3468 alignments, with 40,773 members. There are 2106 family, 1012
superfamily and 350 homology domain alignments. These alignments are
curated and contain only representative sequences; alignment entries are
not necessarily complete.

The information contained in a PIRALN entry is divided into twelve
sections. The sections are listed below in the order in which they occur
in the entry.

  Header - entry beginning and identifier
  Title - title of the alignment
  Alternate names - alternate names for the group
  Date - creation, sequence revision and text revision dates
  Members - PIR entry codes of protein sequences used in the alignment
  Members Titles - PIR titles of sequences used in the alignment
  Other members - other members of the group not represented on the alignment
  Comment - comment lines
  Keywords - keywords present in all the members of the alignemnt
  Other keywords - keywords not common to every member of the alignment
  Alignment - alignment of sequences
  Matrix - matrix of percent differences

The Alignment database has been integrated with the ATLAS multidatabase
information retrieval system, developed at PIR, which provides full
access to the data. 

The Alignment database can be accessed via the WWW at
www-nbrf.georgetown.edu/pir and the "Atlas of Protein and Genomic
Sequences" CD-ROM available from the PIR-International centers in the
US, Europe, and Japan. For anonymous FTP download go to the PIR FTP site
at address NBRF.Georgetown.edu directory [ANONYMOUS.PIR.ALIGNMENT].

Techical questions regarding PIRALN should be directed to Christopher
Marzec and other questions to Lai-Su Yeh or Geetha Srinivasarao at
E-mail: marzec, yeh or geetha at nbrf.georgetown.edu

Regards,

Christopher R. Marzec
Database Manager
PIR-International Protein Sequence Database
National Biomedical Research Foundation
Washington, DC  20007
MARZEC at NBRF.Georgetown.Edu
voice: (202) 687-2121
fax: (202) 687-1662





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