Free accession software for linux

Plasmidb project is a interface to a simple MySQL database, which itself contains information about projects in molecular biology.
The focus is the data pertaining to bacterial plasmids, but also the protein sequences which are being worked on for a particular project, DNA sequences of target genes.
The database is designed to be extensible, so after learning about how the interface works, a user could add data types in SQL tables and write an interface to be able to edit it easily.
Main features:
- Standard cloning or expression plasmids (e.g. their antibiotic selection markers, any RNA polymerase promoters).
- Database sequences you may be currently working on (their accession numbers, sequences, coding sequences).
- Products you may wish to express or purify from them. e.g. His-tagged protein or RNA run-off transcripts etc.
- Primers you have ordered.
- Restriction enzymes.
- DNA sequencing data.
- Protein prep yields and data about purity.
Despite this being a work-in-progress, I have found the database to be very useful.
The database contains user and session information, so only upon logging-in, can one view and edit the database information.
Enhancements:
- User interface improvements, CSS restyle and many framework improvements are included in this release.
- PDF maps can now be added easily to the list of standard plasmids.
- Many Invitrogen and Novagen plasmids are included in the standard database.
- This is the last major release before migrating to Ruby on Rails.

Bio::Index::Blast is a Perl module with indexes Blast reports and supports retrieval based on query accession(s).

SYNOPSIS

use strict;
use Bio::Index::Blast;
my ($indexfile,$file1, $file2);
my $index = new Bio::Index::Blast(-filename => $indexfile,
-write_flag => 1);
$index->make_index($file1, $file2);

my $id;
my $data = $index->get_stream($id);

my $bplite_report = $index->fetch_report($id);
print "query is ", $bplite_report->query, "n";
while( my $sbjct = $bplite_report->nextSbjct ) {
print $sbjct->name, "n";
while( my $hsp = $sbjct->nextHSP ) {
print "t e-value ", $hsp->P,
}
print "n";
}

This object allows one to build an index on a blast file (or files) and provide quick access to the blast report for that accession. Note: for best results use strict.