ASAP2 is one of the largest databases of alternative splicing for complex genomes (human, mouse, rat, chicken, Drosophila, etc.), and provides convenient software tools for alternative splicing studies.
PYGR is an open source software project to develop graph database interfaces for the popular Python language, with a strong emphasis on bioinformatics applications ranging from genome-wide analysis of alternative splicing patterns, to comparative genomics queries of multi-genome alignment data. We and others have used Pygr successfully for many projects, see the Pygr forum pages for examples.
HIV is the UCLA HIV Positive Selection Mutation Database, which includes positive selection analysis of 50,000 HIV-1 subtype B samples from the U.S. identifying mutations that contribute to drug resistance or viral fitness in HIV protease and reverse transcriptase.
GeneMine is an open-source sequence alignment and structure visualization software.
QPRIMER is a novel, automatic web-based application for designing conserved genomic PCR and RT-PCR primers from multigenome alignments on the web using Pygr and PRIMER3. User-friendly and intuitive graphical interface enable one to browse any genomic location and design conserved PCR primers on the fly without any prior preparation of sequences or multiple alignments. Furthermore, vast amount of primer candidates covering various organisms of same gene can give us multiple choices and flexibility. It usually takes less than 5 seconds to get conserved genomic PCR primers on the fly. The only thing user has to know is gene symbol (or full gene name) or its genomic location as well as target exons/introns.