Category Archives: Bioinformatics

An automated method for detecting alternatively spliced protein domains.

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An automated method for detecting alternatively spliced protein domains.

Bioinformatics. 2018 Jun 01;:

Authors: Coelho V, Sammeth M

Abstract
Motivation: Alternative splicing (AS) has been demonstrated to play a role in shaping eukaryotic gene diversity at the transcriptional level. However, the impact of AS on the proteome is still controversial. Studies that seek to explore the effect of AS at the proteomic level are hampered by technical difficulties in the cumbersome process of casting forth and back between genome, transcriptome and proteome space coordinates, and the naïve prediction of protein domains in the presence of AS suffers many redundant sequence scans that emerge from constitutively spliced regions that are shared between alternative products of a gene.
Results: We developed the AstaFunk pipeline that computes for every generic transcriptome all domains that are altered by AS events in a systematic and efficient manner. In a nutshell, our method employs Viterbi dynamic programming, which guarantees to find all score-optimal hits of the domains under consideration, while complementary optimisations at different levels avoid redundant and other irrelevant computations. We evaluate AstaFunk qualitatively and quantitatively using RNAseq in well-studied genes with AS, and on large-scale employing entire transcriptomes. Our study confirms complementary reports that the effect of most AS events on the proteome seems to be rather limited, but our results also pinpoint several cases where AS could have a major impact on the function of a protein domain.
Availability: The JAVA implementation of AstaFunk is available as an open source project on http://astafunk.sammeth.net.
Contact: micha@sammeth.net.
Supplementary information: Supplementary data are available at Bioinformatics online.

PMID: 29868795 [PubMed – as supplied by publisher]

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Panta rhei (QAlign2): an open graphical environment for sequence analysis.

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Panta rhei (QAlign2): an open graphical environment for sequence analysis.
Bioinformatics. 2006 Apr 1;22(7):889-90
Authors: Sammeth M, Griebel T, Tille F, Stoye J
Abstract
MOTIVATIO…

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Divide-and-conquer multiple alignment with segment-based constraints.

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Divide-and-conquer multiple alignment with segment-based constraints.
Bioinformatics. 2003 Oct;19 Suppl 2:ii189-95
Authors: Sammeth M, Morgenstern B, Stoye J
Abstract
A large number …

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