sim4cc protocols

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sim4cc specifications

Information


Unique identifier OMICS_02145
Name sim4cc
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for sim4cc

sim4cc in pipeline

2014
PMCID: 4038475
PMID: 24875882
DOI: 10.1371/journal.pgen.1004403

[…] vertebrate genome assemblies and gene prediction datasets were queried for parp genes using a combination of blast searches , pairwise comparisons of genomic sequences using dotter and the sim4cc program that aligns reference cdna sequences to genomic sequences from other species. we eliminated from further analysis any parp sequences that contained frameshifts or nonsense mutations, […]


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sim4cc in publications

 (5)
PMCID: 4214606
PMID: 25319552
DOI: 10.1186/1745-6150-9-20

[…] above., we produced a gtf file (macam_annotation_v7.6.8, additional file ) that serves as our annotation of the macam assembly. we used the following procedures to generate this file:, 1. we used sim4cc [] and gmap [] to align transcripts (both rhesus macaque and human) against the macam assembly to identify exon boundaries. for sim4cc, we specified cds ranges for the transcripts […]

PMCID: 4038475
PMID: 24875882
DOI: 10.1371/journal.pgen.1004403

[…] vertebrate genome assemblies and gene prediction datasets were queried for parp genes using a combination of blast searches , pairwise comparisons of genomic sequences using dotter and the sim4cc program that aligns reference cdna sequences to genomic sequences from other species. we eliminated from further analysis any parp sequences that contained frameshifts or nonsense mutations, […]

PMCID: 3475488
PMID: 23105930
DOI: 10.5808/GI.2012.10.1.58

[…] of the constantly updated genome annotation. using two model plant (rice and arabidopsis) genomes, we compared two well-known intron prediction tools: the blast-like alignment tool (blat) and sim4cc. the results showed that each of the tools had its own advantages and disadvantages. blat predicted more than 99% introns of whole genomic introns with a small number of false-positive […]

PMCID: 3143108
PMID: 21726447
DOI: 10.1186/1471-2105-12-274

[…] we aligned the known human mrna sequences from each encode region to the corresponding genomic region of every primate species. the nucleotide sequences of these mrnas were mapped using gmap [] and sim4cc []. where available, the coding regions of these human transcripts were translated into proteins and aligned to the corresponding encode regions in the other primates using pmap (a protein […]

PMCID: 2955710
PMID: 20668003
DOI: 10.1093/dnares/dsq017

[…] cdss. in this pipeline, both ends of truncated cdss are extended so that the complete cdss are obtained. our flcdna mapping pipeline was validated and compared with two other cdna mapping programs—sim4cc and geneseqer—as well as three ab initio gene prediction methods. in addition, we estimated how many sequences would be needed for exhaustive gene identification by interspecies mapping. […]


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sim4cc institution(s)
Department of Computer Science, George Washington University, WA, DC, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA

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