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AGLAM specifications

Information


Unique identifier OMICS_29397
Name AGLAM
Alternative names anchored gapless local alignment of multiple sequences, A-GLAM
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 2.1
Stability Stable
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline John Spouge
  • person_outline Nak-Kyeong Kim

Publication for anchored gapless local alignment of multiple sequences

AGLAM citations

 (4)
library_books

Outer membrane vesicles of Tannerella forsythia: biogenesis, composition, and virulence

2015
PMCID: 4604654
PMID: 25953484
DOI: 10.1111/omi.12104

[…] ted by running a BLASTP analysis of known T. forsythia CTD proteins in strain 92A2 (Veith et al., ) against the new genome of strain ATCC 43037. Furthermore, using previously described CTD sequences, a GLAM2 motif was created and subsequently used in GLAM2Scan (http://meme-suite.org/tools/glam2scan) to confirm positive hits. […]

library_books

PairMotif+: A Fast and Effective Algorithm for De Novo Motif Discovery in DNA sequences

2013
PMCID: 3654438
PMID: 23678291
DOI: 10.7150/ijbs.5786

[…] d EM algorithm to improve initial PWMs. The modification of Gibbs Sampling is described in -. In recent years, Bayesian theory has also been introduced in the field of motif search, such as BayesMD , A-GLAM , SBaSeTraM and BAMBI . Besides the statistical methods, some graph-theoretic methods either based on clustering or on heuristic search are proposed to solve the motif search problem, such as […]

library_books

De Novo Discovery of Differentially Abundant Transcription Factor Binding Sites Including Their Positional Preference

2011
PLoS Comput Biol
PMCID: 3037384
PMID: 21347314
DOI: 10.1371/journal.pcbi.1001070

[…] In this section, we first evaluate the performance of Dispom on the motif level using the metazoan compendium. Second, we compare the performance of the seven de-novo discovery tools A-GLAM, DEME, DME, Gibbs Sampler, Improbizer, MEME, and Weeder with that of Dispom on the BS level utilizing 18 benchmark data sets containing experimentally verified BSs. Finally, we apply Dispom to […]

library_books

MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations

2009
Genome Biol
PMCID: 2718512
PMID: 19409082
DOI: 10.1186/gb-2009-10-5-r46

[…] e mixture model using a PWM model on both strands for the motif sequences and a homogeneous Markov model of order 0 for the flanking sequences similar to MEME, Gibbs Sampler, Improbizer, SeSiMCMC, or A-GLAM. For a given set of BSs, MotifAdjuster tests whether each sequence contains a BS, and it refines the annotations of position and strand for each BS, if necessary, by maximizing the posterior of […]

Citations

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AGLAM institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
AGLAM funding source(s)
Supported by the Intramural Research Program of the National Library of Medicine at the National Institutes of Health.

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