CMSC 838T Project 1

The goal of this assignment is to familiarize yourself with a number of web-based bioinformatic tools, by attempting to discover useful information about some protein sequences from the CASP-5 competition. Present what you discover in a short research-style paper.

Protein Sequences

1. MLISHSDLNQ QLKSAGIGFN ATELHGFLSG LLCGGLKDQS WLPLLYQFSN DNHAYPTGLV QPVTELYEQI SQTLSDVEGF TFELGLTEDE NVFTQADSLS DWANQFLLGI GLAQPELAKE KGEIGEAVDD LQDICQLGYD EDDNEEELAE ALEEIIEYVR TIAMLFYSHF NEGEIESKPV LH

2. TGISRETSSDVALASHILTALREKQAPELSLSSQDLELVTKEDPKALAVALNW DIKKTETVQEACERELALRLQQTQSLHSLR

3. QPAKKTYTWNTKEEAKQAFKELLKEKRVPSNASWEQAMKMIINDPRYSALANLSE KKQAFNAYKVQTEK

4. MSTVTKYFYKGENTDLIVFAASEELVDEYLKNPSIGKLSEVVELFEVFTPQDGRGA EGELGAASKAQVENEFGKGKKIEEVIDLILRNGKPNSTTSSLKTKGGNAGTKAYN

Perform the following analyses for each protein sequence

1. Find similar protein sequences
   • Use BLAST at http://www.ncbi.nlm.nih.gov/BLAST/
     Select "Standard protein-protein BLAST [blastp]"

     Do similar sequences provide clues about target protein function?

2. Find protein family / conserved regions using automated tools
   • Use RPS-BLAST at http://www.ncbi.nlm.nih.gov/BLAST/
     Select "RPS-BLAST"
   • Use HMMER at http://pir.georgetown.edu/
     Select "HMM Domain Search" from "Search and Retrieval" menu

     Does target protein belong to family with known function?

3. Perform multiple sequence alignment to identify conserved regions and infer phylogenetic trees
   • Use CLUSTALW at http://pir.georgetown.edu/
     Select "CLUSTALW Alignment" from "Search and Retrieval" menu

     Use T-Coffee at http://us.expasy.org/

     Select T-COFFEE under "Tools and software packages"

     Should lead to http://www.ch.embnet.org/software/TCoffee.html

     Does multiple sequence alignment uncover strongly conserved region(s)?

     Does inferred phylogenetic tree provide hints as to function?

4. Predict secondary structure, 3D structure
   • Use Swiss-Model at http://us.expasy.org/
     Select Swiss-Model under "Tools and software packages"
     Should lead to http://us.expasy.org/swissmod/SWISS-MODEL.html
     Select "First Approach Mode"
     Select "Forward to PHD secondary structure prediction"

     Use 3D-PSSM at http://www.sbg.bio.ic.ac.uk/~3dpssm/

     Select "Recognise a fold"

     Does protein prediction identify any interesting functions for protein?

5. Look for source of protein in genomic DNA, cDNA
   • Use translated BLAST at http://www.ncbi.nlm.nih.gov/BLAST/
     Select "Protein query - Translated db [tblastn]"
     Select "Choose database", try both the default (nr) and genomic DNA (GSS) only.

     What are possible sources of target protein?

     What species? Genomic DNA or other source?