Bioinformatics
Database search
algorithms
BLAST [ Website ] [ Download ]
BLAST® (Basic Local Alignment Search Tool) is a set of similarity
search programs designed to explore all of the available sequence
databases regardless of whether the query is protein or DNA.
Runs on Solaris.
Pattern recognition and
search algorithms
HMMER [ Website ]
HMMER is an implementation of profile HMM methods for sensitive
database searches using multiple sequence alignments as queries.
Runs on Solaris.
ClustalW [ Website ]
ClustalW is a general purpose multiple sequence alignment program for
DNA or proteins.It produces biologically meaningful multiple sequence
alignments of divergent sequences. It calculates the best match for the
selected sequences, and lines them up so that the identities,
similarities and differences can be seen.
Runs on Solaris.
Emboss [ Website ]
EMBOSS (European Molecular Biology Open Software Suite) is a
software-analysis package. It can work with data in a range of formats
and also retrieve sequence data transparently from the Web. Extensive
libraries are also provided with this package, allowing other
scientists to release their software as open source. It provides a set
of sequence-analysis programs, and also supports all UNIX platforms.
Runs on Solaris.
PSI-BLAST[ Download ]
Position-Specific Iterated (PSI)-BLAST is the most sensitive BLAST
program, making it useful for finding very distantly related proteins.
Use PSI-BLAST when your standard protein-protein BLAST search either
failed to find significant hits, or returned hits with descriptions
such as "hypothetical protein" or "similar to...".
Runs on Solaris.
FASTA[ Download ]
Compares a protein sequence to another protein sequence or to a protein
database, or a DNA sequence to another DNA sequence or a DNA library.
Runs on Solaris.
Statistical Methods of
sequence analysis like Fragmentation and genome wide comparison
GenCore[ Website ]
A comprehensive sequence analysis package for high-throughput
environments.
Runs on Solaris.
Development of
secondary databases from primary sources
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