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Exalign specifications

Information


Unique identifier OMICS_07046
Name Exalign
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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Information


Unique identifier OMICS_07046
Name Exalign
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Exalign

Exalign in publications

 (5)
PMCID: 4931340
PMID: 27357338
DOI: 10.1038/ncomms12085

[…] sequencing using the gs flx titanium rapid library preparation kit and sequenced on the roche 454 platform. the resulting sequencing reads were mapped to the genome using blat, and realigned with exalign to determine the intron/exon boundaries. the expression levels were normalized by dividing the matching reads by the total number of reads obtained for each sample, multiplied by two times […]

PMCID: 3882889
PMID: 24063302
DOI: 10.1186/1471-2164-14-654

[…] similarity at the level of every individual protein-coding exon and very similar cds splice patterns, allowing more flexibility for insertions and deletions than sequence-independent methods such as exalign []. unlike methods that depend on pre-calculated whole-genome alignments to assess intra- or intergenic regions across species [], our software can be applied to any valid sequence, […]

PMCID: 3091683
PMID: 20920313
DOI: 10.1186/1471-2164-11-534

[…] ncbi refseq collection [] with the consequence that for orthologous genes different splicing isoforms may be annotated in different organisms., to investigate the extent of this issue, we used the exalign algorithm [] to compare the full set of human gene structures, defined by mapping human refseq transcripts to the genome, to their murine equivalents, with a twofold goal: first, to assess […]

PMCID: 2996940
PMID: 20598118
DOI: 10.1186/1471-2164-11-412

[…] from other homologs. indeed, this been done successfully in specific case studies of gene families, i.e. chemoreceptors [,], heat shock proteins [], and homeobox genes []. also, an algorithm called exalign has been published where exon-intron gene structures are used to resolve phylogenetic relationships []. this method relies solely on exon lengths and phase, when available, to infer gene […]

PMCID: 2492878
PMID: 18647384
DOI: 10.1186/1471-2148-8-214

[…] pendens) (see additional file , )., figure and additional file show the lengths of introns and exons of a representative sample of the β-hexosaminidase genes examined in this study, obtained with exalign []. within the vertebrate hex1 and hex2 subfamilies, the numbers and lengths of exons are remarkably conserved, together with intron phase. vertebrate hex1 and hex2 isoforms are universally […]


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Exalign institution(s)
Dipartimento di Scienze Biomolecolari e Biotecnologie, University of Milan, Milan, Italy

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