HMMSplicer protocols

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HMMSplicer specifications

Information


Unique identifier OMICS_01241
Name HMMSplicer
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 0.9.5
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Joseph L. DeRisi <>

Publication for HMMSplicer

HMMSplicer in pipelines

 (2)
2014
PMCID: 3990616
PMID: 24743507
DOI: 10.1371/journal.pone.0095057

[…] by blast2go using blast and interproscan and manually using hhsearch with the pfam-a database and psi-blast using the nr database. in addition to the program exonerate used in the maker pipeline, hmmsplicer was used to identify and score possible splice sites and alternately spliced transcripts. the inparanoid algorithm of reciprocal blast searches and clustering was employed as described . […]

2014
PMCID: 3990616
PMID: 24743507
DOI: 10.1371/journal.pone.0095057

[…] branch support estimates. the bayesian majority-rule consensus was then visualized and partially edited using figtree v1.4.0 (rambaut, 2012) and geneious ., putative splice sites were identified by hmmsplicer and grouped by output score into 100-point bins. twelve candidates were selected from the highest bin, with scores of 900–1000. pcr primers were designed by primer3 to span the putative […]


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HMMSplicer in publications

 (9)
PMCID: 4576002
PMID: 26436095
DOI: 10.1155/2015/690873

[…] forms and the means of selective splicing. then the authors described the numerous methods for the read mapping of rna-seq data and alternative types of splicing prediction software. at last, hmmsplicer, soapsplice, tophat, and star were used to evaluate the performance of alternative splicing isoforms detection., the article “microrna promoter identification in arabidopsis using multiple […]

PMCID: 4573434
PMID: 26421304
DOI: 10.1155/2015/831352

[…] effect of these factors on as research was analyzed. using rna-seq data produced by the illumina/solexa sequencing platform as an example, we compared three common splice site prediction programs (hmmsplicer [], soapsplice, and tophat []) under conditions of different depths and sequence read lengths. the performance of each type of software was evaluated under different conditions […]

PMCID: 3990616
PMID: 24743507
DOI: 10.1371/journal.pone.0095057

[…] in c. mellificae and absent in l. major., cis-splicing of introns is extremely rare in previously studied trypanosomatids . to investigate the potential for cis-splicing in c. mellificae we used hmmsplicer and long, paired-end transcriptome sequencing (2×100 nt reads with a 300–350 insert size) to identify potential splicing events in c. mellificae. reads were mapped to the assembled genome […]

PMCID: 3961179
PMID: 24651478
DOI: 10.1371/journal.pcbi.1003517

[…] in its user-friendly pipeline for the analysis of both known and novel splicing events directly from solid bioscope processed rna-seq results (but also from other platforms, such as tophat , hmmsplicer and splicemap ). the obtained analysis results can be directly integrated with alternative exon or junction array datasets. unlike existing rna-seq analytical pipelines, this new version […]

PMCID: 4007998
PMID: 24559473
DOI: 10.1186/1471-2164-15-150

[…] for 135 genes (for an example see figure  c). these data indicate that at least some of the observed nats are polyadenylated., based on the splicing junctions identified from our datasets using hmmsplicer [], we found evidence for antisense spliced junctions in 123 of the 1247 genes with nats (additional file : table s5). thus, at least a portion of the observed nats (~10%) is spliced. […]


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HMMSplicer institution(s)
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA; Biological and Medical Informatics Program, University of California San Francisco, San Francisco, CA, USA; Howard Hughes Medical Institute, Bethesda, MD, USA
HMMSplicer funding source(s)
Supported by the Howard Hughes Medical Institute.

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