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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


Add your version

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 in pipelines

 (8)
2017
PMCID: 5509035
PMID: 28854627
DOI: 10.1093/gbe/evx114

[…] 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 […]

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

[…] 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)., […]

2016
PMCID: 5388426
PMID: 28180286
DOI: 10.1093/nar/gkw969

[…] genomes using bowtie () allowing two mismatched bases in a seed region of 14 where only unique alignments were reported (-n 2 –l 14 –m 1)., data analysis was carried out in r using the bioconductor seqtools () and iranges () packages. total error rates were calculated as the percentage of total reads with a mismatched base at each read position in the alignment, thresholded to a phred quality […]

2016
PMCID: 5388426
PMID: 28180286
DOI: 10.1093/nar/gkw969

[…] (gff3) were downloaded from the ncbi website in order to identify protein coding regions (cdss). aligned locations were identified from the bowtie output using bedtools (), and the bioconductor seqtools () and iranges () packages. transcribed but non-translated regions (utrs) in ecrna were identified using rockhopper (), and an s. cerevisiae s288c utrs () were obtained […]

2014
PMCID: 3963999
PMID: 24663063
DOI: 10.1371/journal.pone.0093215

[…] genes that passed the 95% confidence level in 3 or 4 of the arrays were considered to demonstrate differential expression. these genes were then clustered on the basis of their sequence, using seqtools (http://www.seqtool.dk) to identify unique sequences. gene ontology (go) functions were assigned using blast2go (http://www.blast2go) based on blastx homologies., the 5k microarray was used […]


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SeqTools in publications

 (31)
PMCID: 5923399
PMID: 29614714
DOI: 10.3390/md16040112

[…] haimen, china). the purified pcr products were added to basyl a and ligated into the t-tailed plasmid vector pgem-t for dna sequencing. the predicted protein sequences were analyzed with software seqtools (http://www.bio-soft.net/sms). the novel cdna sequence lt1.3 was identified following a comparison with the sequences available in the genbank nucleotide sequence database […]

PMCID: 5780487
PMID: 29362424
DOI: 10.1038/s41598-018-19862-5

[…] blast.cgi). functional annotations of the proteins were performed with pfam database and the string database. the promoter was predicted with fruitfly promoter search tool (http://www.fruitfly.org/seqtools/promoter.html). nucleotide binding sites were predicted with nsite pred server (http://biomine.cs.vcu.edu), whereas, ligand binding sites were predicted using raptorx binding prediction […]

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

[…] 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. […]

PMCID: 5509035
DOI: 10.1093/gbe/evx114

[…] 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 […]

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

[…] 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., […]


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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).

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