Bioinformatics2go

What's New

Group:

V. Brendel serving as Chair of the iPlant Collaborative Scientific Advisory Board

V. Brendel appointed Consulting Editor of The Plant Cell

Recent publications:

Duvick, J., Standage, D.S., Merchant, N. & Brendel, V.P. (2016) xGDBvm: A Web GUI-driven workflow for annotating eukaryotic genomes in the cloud. The Plant Cell [Advance Publication: 28 March 2016]

Standage, D.S., Berens, A.J., Glastad, K.M., Severin, A.J., Brendel, V.P. & Toth, A.L. (2016) Genome, transcriptom and methylome sequencing of a primitively eusocial wasp reveal a greatly reduced DNA methylaiton system in a social insect. Molecular Ecology [First published: 15 March 2016]

PlantGDB News:

xGDBvm on YouTube

Bioinformatics2go

SAPS, SSPA



Description: SAPS stands for Statistical Analysis of Protein Sequences, and SSPA is an acronym for Significant Segment Pair Alignment. These programs are rather old (see citations), but still in use. I am making the old code available as is for now, hoping for some time soon to update the code. In the meantime, give me feedback and suggestions! Volker Brendel, December 16, 2008.

Citations: SAPS - Brendel, V., Bucher, P., Nourbakhsh, I.R., Blaisdell, B.E. & Karlin, S. (1992) Methods and algorithms for statistical analysis of protein sequences. Proc. Natl. Acad. Sci. USA 89, 2002-2006. [PubMed ID: 1549558] [PDF]; SSPA - Karlin, S., Weinstock, G. & Brendel, V. (1995) Bacterial classifications derived from RecA protein sequence comparisons. J. Bacteriol. 177, 6881-6893. [PubMed ID: 7592482]

Web Implementations: SAPS @ EBI; SAPS @ Mobyle

Download: Download SAPS-SSPA