SeqTools statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

SeqTools specifications

Information


Unique identifier OMICS_23182
Name SeqTools
Software type Application/Script, Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Input format GFF3/FASTA,FASTA+FASTA, STOCKHOLM,MSF,SELEX,FASTA
Output format STOCKHOLM,MSF,SELEX,FASTA,PDF
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License GNU General Public License version 3.0
Computer skills Medium
Version 4.37.0
Stability Stable
Requirements
GTK
Maintained Yes

Subtool


  • Blixem

Versioning


No version available

Maintainer


  • person_outline Gemma Barson

Additional information


ftp://ftp.sanger.ac.uk/pub/resources/software/seqtools/Docs/User_doc/index.html

Publication for SeqTools

SeqTools citations

 (20)
library_books

Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica

2017
BMC Genomics
PMCID: 5567635
PMID: 28830347
DOI: 10.1186/s12864-017-4067-x

[…] atenated genomic reference using Bowtie2. The resulting .bam files were sorted with samtools. Using the custom Perl script SeparateHomeolog2Sam (https://github.com/aubombarely/GenoToolBox/blob/master/SeqTools/SeparateHomeolog2Sam) we separated the mapped homoeologous reads of one of the biological replicates of RNAseq data of each accession into separate files [], effectively removing the A. areno […]

library_books

The Mitonuclear Dimension of Neanderthal and Denisovan Ancestry in Modern Human Genomes

2017
Genome Biol Evol
PMCID: 5509035
DOI: 10.1093/gbe/evx114

[…] to the Neanderthal (http://cdna.eva.mpg.de/neandertal/altai/AltaiNeandertal/VCF) and Denisovan (http://cdna.eva.mpg.de/denisova/VCF/hg19_1000g/) data sets, using a custom tool called vcf2Fasta in the seqTools_v2.2 package (https://github.com/jsharbrough/seqTools). Variants were filtered based on basecall quality (≥Q30) and depth (≥10×). We mapped N-mt RefSeq genes to the HuRef alternate genome ass […]

library_books

A reference genome for Nicotiana tabacum enables map based cloning of homeologous loci implicated in nitrogen utilization efficiency

2017
BMC Genomics
PMCID: 5474855
PMID: 28625162
DOI: 10.1186/s12864-017-3791-6

[…] ng the SNPs, filtering them based on the read coverage and the allele frequency and applying the Perl script Vcf4FastaCorrection (available from https://github.com/aubombarely/GenoToolBox/blob/master/SeqTools/Vcf4FastaCorrection). The resulting WGS assembly contained 440,772 contigs/scaffolds and covered 4,145,428,719 bp (3,510,246,061 bp of which were defined), with an N50 of 334,966 bp. […]

library_books

MicroRNA 144 is regulated by CP2 and decreases COX 2 expression and PGE2 production in mouse ovarian granulosa cells

2017
PMCID: 5386473
PMID: 28182010
DOI: 10.1038/cddis.2017.24

[…] programs.html) was used to predict the transcription factor binding sites in the promoters of both mouse miR-144 and pig miR-144. Neural network promoter prediction software (http://www.fruitfly.org/seqtools/promoter.html) was used to analyze the potential promoters, and TargetScan (http://www.targetscan.org/) was used to predict the potential target genes of miRNAs. […]

call_split

Molecular diversity of α gliadin expressed genes in genetically contrasted spelt (Triticum aestivum ssp. spelta) accessions and comparison with bread wheat (T. aestivum ssp. aestivum) and related diploid Triticum and Aegilops species

2016
PMCID: 5104789
PMID: 27942245
DOI: 10.1007/s11032-016-0569-5
call_split See protocol

[…] oEdit v7.1.11 (Hall ). The identification of nucleic and amino acid sequences present in more than one copy, as well as the elaboration of clusters grouping identical sequences, were carried out with SeqTools v8.4.042 (http://www.seqtools.dk/). This software was also used to search for homologies with all α-gliadin proteins in GenBank via a BLASTP analysis (date of analysis: 23 October 2015).The a […]

library_books

Misincorporation by RNA polymerase is a major source of transcription pausing in vivo

2016
Nucleic Acids Res
PMCID: 5388426
PMID: 28180286
DOI: 10.1093/nar/gkw969

[…] identified using samtools and bcftools following the method of Li (,). The positions of specific misincorporations (for instance G>A) were then mapped to the reference genomes using the BioConductor seqTools () and IRanges () packages, excluding those at positions with identified mutations. Misincorporation hotspots for the EcΔGre and ScΔTFIIS datasets were defined as having >50 misincorporations […]

Citations

Looking to check out a full list of citations?

SeqTools institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
SeqTools funding source(s)
Supported by the Wellcome Trust Grant (098051); and the National Human Genome Research Institute Grant (5U54HG00455-04).

SeqTools reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SeqTools