wise
comparison of biopolymers, like DNA and protein sequences
Command lineScience
Not tested on a device yet. What that means
Commands in the package
dbadnalestwiseestwisedbgenewisegenewisedbgenomewisepromoterwisepswpswdbscanwisescanwise_server
About wise
From Debian's package description
Wise2 is a package focused on comparisons of biopolymers, commonly DNA and protein sequences. There are many other packages which do this, probably the best known being BLAST package (from NCBI) and the Fasta package (from Bill Pearson). There are other packages, such as the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused on hidden Markov models (HMMs) of biopolymers.
Wise2's particular forte is the comparison of DNA sequence at the level of its protein translation. This comparison allows the simultaneous prediction of say gene structure with homology based alignment.
Wise2 also contains other algorithms, such as the venerable Smith-Waterman algorithm, or more modern ones such as Stephen Altschul's generalised gap penalties, or even experimental ones developed in house, such as dba. The development of these algorithms is due to the ease of developing such algorithms in the environment used by Wise2.
Wise2 has also been written with an eye for reuse and maintainability. Although it is a pure C package you can access its functionality directly in Perl. Parts of the package (or the entire package) can be used by other C or C++ programs without namespace clashes as all externally linked variables have the unique identifier Wise2 prepended.
From Debian's description of the wise package, under that package's license.
Dependencies
Depends on
libc6libglib2.0-0t64wise-data
Related apps
- snaplocation of genes from DNA sequence with hidden markov modelCommand line
- exonerategeneric tool for pairwise sequence comparisonCommand line
- fsaFast Statistical Alignment of protein, RNA or DNA sequencesCommand line
- hmmerprofile hidden Markov models for protein sequence analysisCommand line
- muscleMultiple alignment program of protein sequencesCommand line
- clustaloGeneral-purpose multiple sequence alignment program for proteinsCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the wise package, under that package's license.
- Description: Debian's description of the wise package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
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