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[ Source: wise  ]

Package: wise (2.4.1-8 and others)

comparison of biopolymers, commonly DNA and protein sequences

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.

Tags: Field: Biology, Bioinformatics, Implemented in: C, User Interface: Command Line, Role: Program, Scope: Utility, Purpose: Comparing

Other Packages Related to wise

  • depends
  • recommends
  • suggests
  • dep: hurd [hurd-i386]
    The GNU Hurd
    also a virtual package provided by hurd-udeb
  • dep: libc0.1 (>= 2.7) [kfreebsd-amd64, kfreebsd-i386]
    GNU C Library: Shared libraries
    also a virtual package provided by libc0.1-udeb
  • dep: libc0.3 (>= 2.10) [hurd-i386]
    GNU C Library: Shared libraries
    also a virtual package provided by libc0.3-udeb
  • dep: libc6 (>= 2.10) [hppa]
    GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb
    dep: libc6 (>= 2.4) [mips, powerpc]
    dep: libc6 (>= 2.5) [avr32]
    dep: libc6 (>= 2.5-5) [m68k]
    dep: libc6 (>= 2.7) [amd64, armel, i386, mipsel, s390, sparc]
  • dep: libc6.1 (>= 2.7) [alpha, ia64]
    GNU C Library: Shared libraries
    also a virtual package provided by libc6.1-udeb
  • dep: libglib1.2ldbl (>= 1.2.10-18) [m68k]
    The GLib library of C routines
  • dep: libglib2.0-0 (>= 2.12.0) [not m68k]
    The GLib library of C routines
  • rec: wise-doc (= 2.4.1-6)
    documentation for the wise package
  • sug: wise-doc (= 2.4.1-8)
    documentation for the wise package

Download wise

Download for all available architectures
Architecture Version Package Size Installed Size Files
alpha 2.4.1-8 5,609.3 kB15572 kB [list of files]
amd64 2.4.1-8 4,414.2 kB12492 kB [list of files]
armel 2.4.1-8 4,684.0 kB11588 kB [list of files]
avr32 (unofficial port) 2.4.1-8 5,551.7 kB10332 kB [list of files]
hppa 2.4.1-8 4,915.4 kB12452 kB [list of files]
hurd-i386 2.4.1-8 3,926.9 kB11148 kB [list of files]
i386 2.4.1-8 3,921.7 kB11128 kB [list of files]
ia64 2.4.1-8 7,756.1 kB26592 kB [list of files]
kfreebsd-amd64 2.4.1-8 4,411.8 kB12708 kB [list of files]
kfreebsd-i386 2.4.1-8 3,920.4 kB11298 kB [list of files]
m68k (unofficial port) 2.4.1-6 3,178.3 kB10364 kB [list of files]
mips 2.4.1-8 4,540.2 kB14676 kB [list of files]
mipsel 2.4.1-8 4,563.6 kB14676 kB [list of files]
powerpc 2.4.1-8 4,524.3 kB12408 kB [list of files]
s390 2.4.1-8 4,568.0 kB11912 kB [list of files]
sparc 2.4.1-8 3,795.6 kB10840 kB [list of files]