ANN-Spec statistics

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ANN-Spec specifications

Information


Unique identifier OMICS_06285
Name ANN-Spec
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for ANN-Spec

ANN-Spec in publications

 (16)
PMCID: 5439287
PMID: 27497616
DOI: 10.1093/bfgp/elw030

[…] discovery has been tackled using a myriad of algorithmic techniques, such as expectation maximization (meme []), gibbs sampling (alignace []), efficient enumeration (amadeus []) and neural networks (ann-spec []). methods that use weights or a ranked list of genes include drim [] and matrixreduce []. a survey of motif finding tools can be found in [, ]., the problem of inferring a motif […]

PMCID: 3603212
PMID: 22517426
DOI: 10.1093/bib/bbs016

[…] (or no occurrence) of a motif within the same sequence (algorithm known as ‘motif sampler’). modifications of the basic gibbs sampling technique were also described for example in alignace [] and ann-spec []., the function used to assess profile significance should simultaneously take into account both how much each column of the profile is conserved and how the nucleotide frequencies […]

PMCID: 2881025
PMID: 20459624
DOI: 10.1186/1471-2164-11-286

[…] to deduce the form or motif of the binding site which is then used to identify sites in other sequences — reviews of these methods are given in [,]. these methods include weeder [], meme [], ann-spec [], morph [] and glam []. some authors have proposed a statistical test to decide whether a region of dna is a regulatory region: two methods [,] tested on fly data have been motivated […]

PMCID: 2848242
PMID: 20214810
DOI: 10.1186/1471-2164-11-161

[…] nsmce4a). the three tfs that bind to those sites were found to be active in the adipocytokine signaling pathway on the basis of a crsd search []. comparison of the motifs predicted ab initio using ann-spec [] with known tfbss identified elf1- and sp1-like sites as matches, indicating that elf1 and sp1 tfs regulate genes in the livr cluster (additional file ). as corroborating evidence, an elf1 […]

PMCID: 2763271
PMID: 19893611
DOI: 10.1371/journal.pgen.1000709

[…] , siggia and desplan laboratories in combination with the transfac public database and additional experimentally confirmed tfbss found in literature searches as described in the section (). ann-spec was used to align the tfbs sequences and develop an alignment matrix and a position weight matrix (pwm) for each of six tfs: bicoid (bcd), even-skipped (eve), fushi-tarazu (ftz), hunchback […]


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ANN-Spec institution(s)
Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark

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