Tag: GeneSeqer

ASpipe 2.1.8 – Process GeneSeqer/GMAP Alignments & Identify Alternative Splicing

ASpipe 2.1.8

:: DESCRIPTION

ASpipe (alternative splicing) is a pipeline to process GeneSeqer/GMAP alignments and identify alternative splicing (AS) events from the alignments.ASpipe extracts coordinates and scores for high-quality intron/exon/alignments from the original program outputs and stores them in MySQL5.0 databases.

::DEVELOPER

The Brendel Group @ Indiana University

:: REQUIREMENTS

:: DOWNLOAD

ASpipe

:: MORE INFORMATION

Citation

Wang, B.-B., O’Toole, M., Brendel, V. & Young, N.D. (2008)
Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes.
BMC Plant Biol. 8:17.

GeneSeqer 20140226 – Gene Identification Tool

GeneSeqer 20140226

:: DESCRIPTION

GeneSeqer is a gene identification tool based on spliced alignment or “spliced threading” of ESTs with a genomic query sequence. In a spliced alignment, aligned residues in the genomic sequence are assigned exon status. Introns are identfied as large gaps in the alignment, typically (but not necessarily) flanked by the consensus GT and AG dinucleotides at the donor and acceptor sites, respectively. The optimal alignment is derived by scoring for both sequence similarity and potential splice site strength. The program is designed to handle alignment of a large number of ESTs on a long genomic query sequence (BAC size). Therefore, the ESTs are pre-screened, and only ESTs with sufficient significant matching are fully aligned.

::DEVELOPER

The Brendel Group @ Indiana University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GeneSeqer

:: MORE INFORMATION

Citation

Brendel, V., Xing, L. and Zhu, W.
Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus.
Bioinformatics 20(7), 1157-1169 (2004).

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