A DNA/protein sequence retrieval system: an Xtpanel application

Akihiro Oda[1]
Minoru Kanehisa[2]

[1] Information System Department
Molecular Biology Research Department
Nippon Shinyaku Co., LTD.
Nishiohji-hachijyo, Minami-ku Kyoto 601, Japan
[2] Institute for Chemical Research
Kyoto University
Uji Kyoto 611, Japan


Computational methods are indispensable tools for researchers who determine a new nucleic acid or protein sequence. Such methods are used to obtain informaion to help identify and annotate the new sequence. Database searching is currrently the most popular way to get this information. Using homology- search programs such as FASTA or BLAST, one can search a database for sequences similar to a given query sequence. In addition, the alignment of multiple nucleotide or amino acid sequences is important for drawing phylogenetic trees and for predicting the structure of proteins. The multiple sequence alignment of proteins is also used to discover motifs and biologically important patterns.
We have developed a retrieval system for nucleic acid and/or protein sequences. The system is an Xtpanel application that runs on Sun Workstations with the X-Window system. Xtpanel, which is written by Steve Cole and Dave Nichols of Stanford University, allows one to build interactive X-Window system interfaces without having to do conventional X programming.
It supports FASTA and BLAST for homology searches, bfind and bget for database entry retrievals, and CLUSTAL V for multiple sequence alignments.