Project Trans Membrane

Project Trans-membrane MSA (Jia Ming).

Project Trans-membrane MSA (Jia Ming)

Project Name: Trans-membrane Multiple Sequence Alignment

Project Start Date: 05. 2009

Questions: t-coffee default: gapopen, gapextend =0?

Lab-Book:

Data set: Collect odorant receptor genes for

BaliBASE 2.0, Reference 7, Transmembrane Protein 8 families 435 proteins Drosophila, Mosquito, Human

Method: Perform T-Coffee in three different modes #1; default T-coffee -> 36 #2: T-Coffee -template_mode BLAST -> 43 simple way: -produce the probabilistic PHAT matrix

• hh=>phat anything else blosum #3: t_coffee 1aab_ref1.pep -template_mode BLAST, TM #4: t_coffee 1aab_ref1.pep -template_mode BLAST, PSITM default, incorporating topology prediction, PSI-Blast profile Incorporate other topology prediction result by using consistency based approach. Discuss accuracy about diffierernt TM topology combination Construct a benckmark for trans-membrane MSA Modify Seqan:T-coffee code, write a class for incorporating structural information

Results:

• Comparison between the PSITM and other MSAs

Links:

• BaliBASE2.0
• Server PRALINE_TM
• Paper PRALINE_TM

Bibliography:

Walter Pirovano, K. Anton Feenstra, Jaap Heringa: PRALINETM: a strategy for improved multiple alignment of transmembrane proteins. Bioinformatics 24(4): 492-497 (2008)

PHAT: a transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane. Ng PC, Henikoff JG, Henikoff S. Bioinformatics. 2000 Sep;16(9):760-6. Erratum in: Bioinformatics 2001 Mar;17(3):290.