Database and Information Management

[*] ACeDB was originally developed for the C.elegans genome project, from which its name was derived (A Caenorhabditis Elegans DataBase). However, the tools in it have been generalised to be much more flexible and the same software is now used for many different genomic databases from bacteria to fungi to plants to man. ACeDB can also be accessed via WebACeDB.
[*] New! BioJava Project is an open-source project dedicated to providing Java tools for processing biological data. This will include objects for manipulating sequences, file parsers, CORBA interoperability, access to ACeDB, dynamic programming, and simple statistical routines.
[*] Blast (Basic Local Alignment Search Tool) is a sequence database search program.
[*] Cambridge Structural Database System (CSD) contains crystal structure information for over 175,000 organic and organometallic compounds. All of these crystal structures have been analysed using X-ray or neutron diffraction techniques.
[*] DBWatcher is a program handling periodic BLAST searches to find similarities to your own sequences. It keeps track of the previous searches and only performs new ones when necessary (i.e. when the database has been updated, the sequence has been modified, or when settings have been changed).
[*] DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor. It can be used to edit protein, DNA or RNA alignments. The structure of the molecules can be incorporated in the alignment.
[*] fetch (Free Extraction Tool for Computational Humanoid) is an easy swissprot protein sequence retrieval utility. It is text based. It is available in Perl and Linux binary format compiled by Perl compiler. It can extract any sequences you want as long as they are in swissprot sequence database(primarily). Swissprot is distibuted as a file called "seq.dat" (around 100 mb, Oct. 1996). fetch creates an index file (seq.idx) for the entries for speed.
[*] FPC (fingerprinted contigs) is an interactive program for building contigs from fingerprinted clones, where the fingerprint for a clone is a set of restriction fragments. FPC has an algorithm to automatically cluster clones into contigs based on their probability of coincidence score. For each contig, it builds a consensus band (CB) map which is similar to a restriction map but it does not try to resolve all the errors.
[CM] GeneMine GeneMine[tm] is the first expert bioinformatics data mining system to automatically query multiple independent sources.
[CM] New! GeneMine is the first expert bioinformatics data mining system to automatically query multiple independent sources. Has been designed to provide users with a set of features that can be readily customized to their specifications. Can also be configured to take advantage of new sequence alignment algorithms, protein structure modeling algorithms, and other analysis tools.
[GPL] GPeriodic acts as a periodic table reference and allows you to browse through the table of elements, and view detailed information on each of the elements. 118 elements are currently listed.
[*] LASSAP (LArge Scale Sequence compArison Package) is an extensible, high performance , parallel sequence comparison software. It currently implements all major sequence comparison algorithms (Fasta, Blast, Smith/Waterman), and others string matching and pattern matching algorithms. It is both an integrated software for end-users and a framework allowing the integration and the combination of new algorithms. In addition to usual data banks scanning, LASSAP can fit special needs of high throughput sequencing centers, Bioinformatics Institutes and scientific projects requiring a lot of computation.
[*] Naccess is a stand alone program that calculates the accessible area of a molecule from a PDB (Protein Data Bank) format file. It can calculate the atomic and residue accessiblities for both proteins and nucleic acids, and is available for free from this site for researchers at academic and non profit-making institutions.
[*] Pfarm is a database of multiple alignments of protein domains or conserved protein regions. Hopefully they represent some evolutionary conserved structure which has implications for the protein's function. Pfam is actually formed in two separate ways. Pfam-A are accurate human crafted multiple alignments whereas Pfam-B is an automatic clustering of the rest of swissprot using the program Domainer.
[*] Pombase is a compilation of data relating to the organism Schizosaccharomyces pombe
[*] Sequin is a program designed to aid in the submission of sequences to the GenBank, EMBL, and DDBJ sequence databases. It is capable of handling simple submissions which contain a single short mRNA sequence, and complex submissions containing long sequences, multiple annotations, segmented sets of DNA, or phylogenetic and population studies.
[*] Wormpep contains predicted proteins from the Caenorhabditis elegans genome sequencing project. All these proteins are stored and analysed in ACEDB, and are dumped out quarterly to be released as Wormpep.