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[ Source: wise  ]

Package: wise (2.4.1-7 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 enviroment 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
  • dep: libc0.1 (>= 2.3) [kfreebsd-amd64, kfreebsd-i386]
    GNU C Library: Shared libraries
    also a virtual package provided by libc0.1-udeb
  • dep: libc0.3 (>= 2.9) [hurd-i386]
    GNU C Library: Shared libraries
    also a virtual package provided by libc0.3-udeb
  • dep: libc6 (>= 2.3) [amd64]
    GNU C Library: Shared libraries
    also a virtual package provided by libc6-udeb
    dep: libc6 (>= 2.3.6-6~) [i386]
    dep: libc6 (>= 2.4) [armel, mips, mipsel, powerpc, s390]
    dep: libc6 (>= 2.5) [hppa]
    dep: libc6 (>= 2.5-5) [m68k]
    dep: libc6 (>= 2.6) [sparc]
  • dep: libc6.1 (>= 2.3) [ia64]
    GNU C Library: Shared libraries
    also a virtual package provided by libc6.1-udeb
    dep: libc6.1 (>= 2.4) [alpha]
  • 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 (= 2.4.1-7)
    documentation for the wise package

Download wise

Download for all available architectures
Architecture Version Package Size Installed Size Files
alpha 2.4.1-7 5,632.6 kB15548 kB [list of files]
amd64 2.4.1-7 4,407.3 kB12472 kB [list of files]
armel 2.4.1-7 4,671.6 kB11584 kB [list of files]
hppa 2.4.1-7 4,899.3 kB12432 kB [list of files]
hurd-i386 2.4.1-7 3,915.7 kB11136 kB [list of files]
i386 2.4.1-7 3,912.4 kB11124 kB [list of files]
ia64 2.4.1-7 7,748.4 kB26576 kB [list of files]
kfreebsd-amd64 2.4.1-7 4,405.5 kB12708 kB [list of files]
kfreebsd-i386 2.4.1-7 3,910.2 kB11296 kB [list of files]
m68k (unofficial port) 2.4.1-6 3,178.3 kB10364 kB [list of files]
mips 2.4.1-7 4,529.1 kB14660 kB [list of files]
mipsel 2.4.1-7 4,552.4 kB14660 kB [list of files]
powerpc 2.4.1-7 4,507.7 kB12388 kB [list of files]
s390 2.4.1-7 4,562.9 kB11908 kB [list of files]
sparc 2.4.1-7 3,784.5 kB10820 kB [list of files]