PhyloCSF protocols

PhyloCSF specifications

Information


Unique identifier OMICS_05865
Name PhyloCSF
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Publication for PhyloCSF

PhyloCSF IN pipelines

 (4)
2017
PMCID: 5450112
PMID: 28558830
DOI: 10.1186/s13058-017-0853-2

[…] lincin lacks the potential to encode any recognizable protein domains. as described previously [19], we further examined the coding potential of lincin using a bioinformatics tool, phylocsf, a comparative genomics method for distinguishing protein-coding and non-coding regions based on their evolutionary signatures characteristic to alignments of conserved coding regions [39]. […]

2017
PMCID: 5890388
PMID: 29657298
DOI: 10.3390/ncrna4010001

[…] and compared using cufflinks [52]. cage data for analysis of htapas and htert tsss in gm12878 cells were downloaded from the encode consortium (encode accession number encsr000cka). , phastcons, phylocsf and phylop scores, based on multi-way alignment of 20 mammalian genomes, were aggregated over the htapas locus (chr5:1295329-1296947, 1619 positions), htert exons (nm_198253 exons annotated […]

2016
PMCID: 5100587
PMID: 27365046
DOI: 10.1093/nar/gkw587

[…] monkey were also identified. transcripts >200nt were identified as lncrnas if they did not overlap with known genomic annotations from the ensembl database and no coding potential was assessed by phylocsf. next, the reads per kilo base of model per million base pairs sequenced (rpkm) was used to quantify the gene or lncrna expression levels (25)., embryo development genes were also obtained […]

2013
PMCID: 3905897
PMID: 24038472
DOI: 10.1093/nar/gkt818

[…] and non-coding transcripts based directly on rna-seq data (67,70). other programs or pipelines can also filter lncrnas de novo from rna-seq data, of which codon substitution frequency (71) and phylocsf (72) are most typical. many mouse development studies used these tools to identify and filter novel lncrnas based on high-throughput transcriptomic data (4,28,67,70). however, […]

PhyloCSF institution(s)
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA

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