Table 1.
Computational Tools Used for Sequence Analysis
| Program/Resource | Description | URL/availability |
| PressDB | makes local BLAST database from file of fasta sequences | see BLASTN URL below |
| BLASTN | locally aligns a query sequence against a database of sequences | http://www.ncbi.nlm.nih.gov/BLAST ftp://ncbi.nlm.nih.gov/pub/blast |
| PowerBLAST | BLAST-like program with graphical output plus repeat filtering functions | ftp://ncbi.nlm.nih.gov/pub/sim2/PowerBlast |
| Musk | program for viewing ASN.1 objects | ftp://ncbi.nlm.nih.gov/pub/sim2/PowerBlast |
| Sequin | sequence annotation/submission tool | ftp://ncbi.nlm.nih.gov/sequin |
| dbEST | database of ESTs | http://www.ncbi.nlm.nih.gov/dbEST |
| dbSTS | database of STSs | http://www.ncbi.nlm.nih.gov/dbSTS |
| nr | nonredundant database of nucleotide sequences | http://www.ncbi.nlm.nih.gov |
| SEG | identifies regions of low complexity in protein and nucleic acid sequences | ftp://ncbi.nlm.nih.gov/pub/seg/seg |
| Perl | powerful scripting language with strong text-handling features | http://www.perl.org |
| AnnotGeneScan | Perl script that generates ASN.1 output from GenScan textual output | http://www.ncbi.nlm.nih.gov/Kuehl/prefinished |
| AnnotGRAIL | Perl script that generates ASN.1 output from GRAIL textual output | http://www.ncbi.nlm.nih.gov/Kuehl/prefinished |
| AnnotMZEF | Perl script that generates ASN.1 output from MZEF textual output | http://www.ncbi.nlm.nih.gov/Kuehl/prefinished |
