ReadSeq protocols

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ReadSeq specifications

Information


Unique identifier OMICS_17576
Name ReadSeq
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline LoopDLoop Team <>

Additional information


http://iubio.bio.indiana.edu/soft/molbio/readseq/version2/Readseq2-help.html

Information


Unique identifier OMICS_17576
Name ReadSeq
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 2.1.3
Stability Stable
Source code URL http://iubio.bio.indiana.edu/soft/molbio/readseq/
Maintained Yes

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Documentation


Maintainer


  • person_outline LoopDLoop Team <>

Additional information


http://iubio.bio.indiana.edu/soft/molbio/readseq/version2/Readseq2-help.html

Publication for ReadSeq

ReadSeq in pipeline

2015
PMCID: 4493790
PMID: 26093024
DOI: 10.1093/jxb/erv283

[…] grass genomic regions were selected based on the highest score and >70% query bac coverage. the gene and repeatmasker te annotation gffs were retrieved and reformatted as genbank files using readseq v.2.1.30. manual corrections were made to genbank file tags and field names so that they were readable by mauve. the chromosome region were submitted to the mauve 2.3.1 () progressive mauve […]


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ReadSeq in publications

 (16)
PMCID: 4604477
PMID: 26462752
DOI: 10.1038/srep15188

[…] and considering a region to be unique if it had a bsr value > 0.8 in target genomes and a bsr value < 0.4 in all non-target genomes., the fasta output of nasp was converted to nexus using readseq. the retention index for each base was then calculated with paup v4a140; the specific paup commands are publicly available (https://gist.github.com/jasonsahl/a66afa55371d7d916a0e). the snp […]

PMCID: 4493790
PMID: 26093024
DOI: 10.1093/jxb/erv283

[…] grass genomic regions were selected based on the highest score and >70% query bac coverage. the gene and repeatmasker te annotation gffs were retrieved and reformatted as genbank files using readseq v.2.1.30. manual corrections were made to genbank file tags and field names so that they were readable by mauve. the chromosome region were submitted to the mauve 2.3.1 () progressive mauve […]

PMCID: 4428239
PMID: 25896062
DOI: 10.1186/s12864-015-1536-y

[…] url, http://www.ncbi.nlm.nih.gov/nuccore?term=ds236884:ds264093[pacc] as genomic scaffolds. from the same site the annotated genome was downloaded in genbank(full) format then converted to gff using readseq (http://iubio.bio.indiana.edu/soft/molbio/readseq/java/). b. malayi proteins sequences were downloaded […]

PMCID: 4403034
PMID: 25914447
DOI: 10.6026/97320630011131

[…] a normalized z-score >1 was considered optimal. the entire top 10 template alignment file (.ali) was used for building loops using modeller program. the fasta was converted to pir using embl׳s readseq algorithm. structure similarity was performed by using the profile.build (), an inbuilt command in modeller. the build_profile.py was then used for the local dynamic algorithm to identify […]

PMCID: 4347569
PMID: 25737742
DOI: 10.1186/s13039-015-0112-0

[…] human genome browser (http://genome.ucsc.edu/), repeat masker web server (http://www.repeatmasker.org/cgi-bin/webrepeatmasker), clustalw2 (http://www.ebi.ac.uk/tools/clustalw2/index.html) and www readseq sequence conversion (http://www-bimas.cit.nih.gov/molbio/readseq).table 3, to determine which yq11 sequences were contained in the der(x) chromosome, 19 sequence tagged sites (sts) on various […]


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ReadSeq institution(s)
Bioinformatics group, Biology Department & Centre Genomics & Bioinformatics, Indiana University, Bloomington, IN, USA

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