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SLAM specifications

Information


Unique identifier OMICS_07790
Name SLAM
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No

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Publications for SLAM

SLAM citations

 (9)
library_books

Recent Applications of Hidden Markov Models in Computational Biology

2016
PMCID: 5172443
PMID: 15629048
DOI: 10.1016/S1672-0229(04)02014-5

[…] found, the hmm can be retrained to include them, new multiple alignments are made, and the process is repeated., alexandersson et al. implemented a cross-species gene finding and alignment program slam using gphmm, which simultaneously aligns and predicts genes in two orthologous sequences. the input to slam consists of two sequences and an approximate alignment . the approximate alignment […]

library_books

Genome Majority Vote Improves Gene Predictions

2011
PLoS Comput Biol
PMCID: 3219611
PMID: 22131910
DOI: 10.1371/journal.pcbi.1002284

[…] multiple genomes for improving gene predictions. numerous methods have used conservation patterns in pairwise sequence alignments to distinguish coding from non-coding regions in eukaryotic (slam , sgp2 , twinscan , , , guigó et al. ) or prokaryotic genomes (walker et al. ,). the use of more than two sequences to improve prediction of gene boundaries is a more recent addition., rast […]

library_books

Testing the Coding Potential of Conserved Short Genomic Sequences

2010
Adv Bioinformatics
PMCID: 2834954
PMID: 20224812
DOI: 10.1155/2010/287070

[…] related species (e.g., mouse), one can combine the conserved information of the two species to develop a more refined probability models for the gene portions (rosetta [], cem [], twinscan [], slam [], and sgp2 [–]). while these approaches have been effective in predicting genes, a noticeable drawback is that the more refined a probability model is, the more constraints there are for a dna […]

library_books

Hidden Markov Models and their Applications in Biological Sequence Analysis

2009
Curr Genomics
PMCID: 2766791
PMID: 20190955
DOI: 10.2174/138920209789177575

[…] for comparative gene prediction by combining the pair-hmm (widely used for sequence alignment and comparison) and the generalized hmm (used by many gene finders). comparative gene-finders such as slam [] and twain [] are implemented based on the gphmm framework. a similar model has been also proposed in [] to compare two dna sequences and jointly analyze their gene structures., although […]

library_books

Reranking candidate gene models with cross species comparison for improved gene prediction

2008
BMC Bioinformatics
PMCID: 2587481
PMID: 18854050
DOI: 10.1186/1471-2105-9-433

[…] of candidate gene models., cross-species comparisons have been shown to be effective in locating genes and predicting gene structures. de novo gene finders such as sgp2 [], twinscan [,], nscan [], slam [], saga [], dogfish [], exoniphy [], shadower [], contrast [] have improved upon ab initio gene finders through comparison with genomic sequences of reference species, capturing phylogenetic […]

library_books

Improving the specificity of exon prediction using comparative genomics

2008
BMC Genomics
PMCID: 2559877
PMID: 18831778
DOI: 10.1186/1471-2164-9-S2-S13

[…] [,]. recently, a new class of gene-prediction algorithms which exploits the power of comparative genomics have been developed, these include but are not limited to rosetta [], cem [], twinscan [], slam [], and sgp2 []. relative to the single genome approaches, these programs have substantially reduced the number of false predictions, (i.e. improved specificity), but the reduction is not enough […]


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SLAM institution(s)
Department of Mathematics, UC Berkeley, USA

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