套件：sim4db（0~20150903+r2013-9 以及其他的）

[ 原始碼： 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.

其他與 sim4db 有關的套件

• dep: libc6 (>= 2.38) [除 alpha, ia64, sh4]

  GNU C 函式庫：共用函式庫
  同時作為一個虛擬套件由這些套件填實： libc6-udeb

  dep: libc6 (>= 2.39) [sh4]

• dep: libc6.1 (>= 2.36) [ia64]

  GNU C 函式庫：共用函式庫
  同時作為一個虛擬套件由這些套件填實： libc6.1-udeb

  dep: libc6.1 (>= 2.38) [alpha]

• dep: libgcc-s1 (>= 3.0) [amd64, arm64, mips64el, ppc64, ppc64el, s390x, x32]

  GCC 支援函式庫

  dep: libgcc-s1 (>= 3.4) [alpha, riscv64, sparc64]

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

  dep: libgcc-s1 (>= 4.2) [i386, ia64, sh4]

• dep: libgcc-s2 (>= 4.2.1) [m68k]

  GCC 支援函式庫

• dep: libgcc-s4 (>= 4.1.1) [hppa]

  GCC 支援函式庫

• dep: libstdc++6 (>= 5.2)

  GNU Standard C++ Library v3

• dep: libunwind8 [ia64]

  library to determine the call-chain of a program - runtime

• rec: kmer-examples

  sample data for kmer suite of tools for DNA sequence analysis

• rec: leaff

  biological sequence library utilities and applications

下載 sim4db

下載可用於所有硬體架構的

硬體架構	版本	套件大小	安裝後大小	檔案
alpha （非官方移植版）	0~20150903+r2013-9	450。7 kB	3，844。0 kB	[檔案列表]
amd64	0~20150903+r2013-9	433。5 kB	3，359。0 kB	[檔案列表]
arm64	0~20150903+r2013-9	411。1 kB	3，519。0 kB	[檔案列表]
armel	0~20150903+r2013-9	378。8 kB	3，059。0 kB	[檔案列表]
armhf	0~20150903+r2013-9	374。8 kB	2，663。0 kB	[檔案列表]
hppa （非官方移植版）	0~20150903+r2013-9	445。2 kB	3，381。0 kB	[檔案列表]
i386	0~20150903+r2013-9	427。5 kB	3，459。0 kB	[檔案列表]
ia64 （非官方移植版）	0~20150903+r2013-8+b3	559。2 kB	4，987。0 kB	[檔案列表]
m68k （非官方移植版）	0~20150903+r2013-9	435。3 kB	3，431。0 kB	[檔案列表]
mips64el	0~20150903+r2013-9	446。8 kB	4，069。0 kB	[檔案列表]
ppc64 （非官方移植版）	0~20150903+r2013-9	447。9 kB	4，863。0 kB	[檔案列表]
ppc64el	0~20150903+r2013-9	475。3 kB	4，799。0 kB	[檔案列表]
riscv64	0~20150903+r2013-9	469。9 kB	3，083。0 kB	[檔案列表]
s390x	0~20150903+r2013-9	403。0 kB	3，379。0 kB	[檔案列表]
sh4 （非官方移植版）	0~20150903+r2013-9	431。7 kB	3，496。0 kB	[檔案列表]
sparc64 （非官方移植版）	0~20150903+r2013-9	412。8 kB	26，032。0 kB	[檔案列表]
x32 （非官方移植版）	0~20150903+r2013-9	441。4 kB	3，311。0 kB	[檔案列表]