PhyloCSF protocols

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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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Publication for PhyloCSF

PhyloCSF in pipelines

 (7)
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 [], 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 []. […]

2017
PMCID: 5721798
PMID: 29133519
DOI: 10.1161/JAHA.117.007431

[…] 2766 distinct multiexon lincrnas that are reliably expressed in human macrophages, of which 861 were previously unannotated (figure ). coding potential for all 2766 lincrnas was further validated by phylocsf, as described in data and the lincrnas with scores higher than the threshold cutoff were listed in table ., among the 2766 lincrnas, 1282 lincrnas were found in all 6 m0, m1, or m2 hmdms, […]

2017
PMCID: 5754203
PMID: 29260710
DOI: 10.7554/eLife.29005.039

[…] generate a consensus annotation set. transcript models were attributed to a rampage tsc if their 5’ end lay within 150 of that tsc. models without a matching tsc were excluded from further analyses. phylocsf was run on these annotation sets and the 15-way multiz whole-genome alignments., we used the meme suite v4.9.0 (primarily fimo and mast) to search promoter regions for a previously published […]

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

[…] and compared using cufflinks []. 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 ()., embryo development genes were also obtained […]


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PhyloCSF in publications

 (98)
PMCID: 5946474
PMID: 29747577
DOI: 10.1186/s12864-018-4754-2

[…] 2823 transcripts were obtained after filter of the low expression transcripts with fpkm < 0.5. finally, coding potential analysis was performed using the software cnci, cpc, pfam-scan, and phylocsf. after being screened by rigorous criteria and four analytic tools, a total of 1376 lncrnas from the tracheal tissue of chickens were identified and subjected to further analysis (fig. ). […]

PMCID: 5940789
PMID: 29739971
DOI: 10.1038/s41598-018-25103-6

[…] cuffmerge, and cuffcompare. the programs coding-non-coding-index (cnci) (version 2), coding potential calculator (cpc) (http://cpc.cbi.pku.edu.cn/) and phylogenetic codon substitution frequency (phylocsf) were used to predict the protein-coding potential of new transcripts with default parameters. the intersection of the results without protein-coding potential yielded lncrna transcripts. […]

PMCID: 5923264
PMID: 29703926
DOI: 10.1038/s41598-018-24863-5

[…] short open reading frame (<300 nt) transcripts. we performed both the coding potential calculator (cpc) and coding-potential assessment tool (cpat) to calculate the coding potential, as well as phylocsf to analyze the conserved regions of the multi-species genome sequence alignment of all candidate transcripts to distinguish the coding and non-coding sequences. furthermore, the transcripts […]

PMCID: 5910401
PMID: 29679004
DOI: 10.1038/s41467-018-04006-0

[…] and quantitative real-time pcr (qpcr) revealed that the 2075-nt linc01138 is the predominant and quite stable transcript in hcc cell lines and hcc tissues (supplementary fig. ). in addition, the phylocsf codon substitution frequency analysis, coding potential assessment tool (cpat), coding potential calculator (cpc) and orf finder software from the national centre for biotechnology […]

PMCID: 5923456
PMID: 29601508
DOI: 10.3390/v10040162

[…] assembled using both scripture (beta2) and cufflinks (v2.1.1) [,]. the distributions of reads for known genes were analyzed using htseq []., four coding potential analysis software packages, cnci, phylocsf with default parameters, cpc and pfam searches with default parameters of −e 0.001 and −dome 0.001, were used to assess the transcript coding potential [,,,]. transcripts that were predicted […]


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

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