What's New

Recent publications:

Wilkerson, M.D., Ru, Y., and Brendel, V.P. (2009) Common introns within orthologous genes: software and application to plants Briefings in Bioinformatics, 10(6), 631-644. [abstract] [PDF]

PlantGDB News:

Community-annotated maize gene models (see an example at ZmGDB) are now displayed at both MaizeGDB and maizesequence.org, by means of Distributed Annotation Service (DAS) (November 21, 2009).

Brachypodium distachyon browser: BdGDB, a genome browser for the model grass species Brachypodium distachyon, is now available, based on the JGI v1.0 8x genome assembly. The assembly displayed comprises 271.15 Mb arranged in 5 pseudochromosomes. Display includes gene models, splice-aligned EST, cDNA, PUT assembly and Arabidopsis and rice predicted proteins (October 30, 2009).

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