Pakket: sim4db (0~20150903+r2013-9)

[ Bron: kmer  ]

batch spliced alignment of cDNA sequences to a target genome

Sim4db performs fast batch alignment of large cDNA (EST, mRNA) sequence sets to a set of eukaryotic genomic regions. It uses the sim4 and sim4cc algorithms to determine the alignments, but incorporates a fast sequence indexing and retrieval mechanism, implemented in the sister package 'leaff', to speedily process large volumes of sequences.

While sim4db produces alignments in the same way as sim4 or sim4cc, it has additional features to make it more amenable for use with whole-genome annotation pipelines. A script file can be used to group pairings between cDNAs and their corresponding genomic regions, to be aligned as one run and using the same set of parameters. Sim4db also optionally reports more than one alignment for the same cDNA within a genomic region, as long as they meet user-defined criteria such as minimum length, percentage sequence identity or coverage. This feature is instrumental in finding all alignments of a gene family at one locus. Lastly, the output is presented either as custom sim4db alignments or as GFF3 gene features.

This package is part of the Kmer suite.

Andere aan sim4db gerelateerde pakketten

• dep: libc6 (>= 2.38)

  GNU C Bibliotheek: Gedeelde bibliotheken
  Ook een virtueel pakket geboden door: libc6-udeb

• dep: libgcc-s1 (>= 3.0) [niet armel, armhf, i386, riscv64]

  GCC support bibliotheek

  dep: libgcc-s1 (>= 3.4) [riscv64]

  dep: libgcc-s1 (>= 3.5) [armel, armhf]

  dep: libgcc-s1 (>= 4.2) [i386]

• dep: libstdc++6 (>= 5.2)

  GNU Standard C++ Library v3

• rec: kmer-examples

  sample data for kmer suite of tools for DNA sequence analysis

• rec: leaff

  biological sequence library utilities and applications

sim4db downloaden

Pakket downloaden voor alle beschikbare platforms

Platform	Pakketgrootte	Geïnstalleerde grootte	Bestanden
amd64	433,5 kB	3.359,0 kB	[overzicht]
arm64	411,1 kB	3.519,0 kB	[overzicht]
armel	378,8 kB	3.059,0 kB	[overzicht]
armhf	374,8 kB	2.663,0 kB	[overzicht]
i386	427,5 kB	3.459,0 kB	[overzicht]
mips64el	446,8 kB	4.069,0 kB	[overzicht]
ppc64el	475,3 kB	4.799,0 kB	[overzicht]
riscv64	469,9 kB	3.083,0 kB	[overzicht]
s390x	403,0 kB	3.379,0 kB	[overzicht]