The following is a short tutorial on how to align a group of sequences with the pima program.
First, Fetch a sequence to use as a query sequence. The GCG program called "fetch" will fetch a sequence from your local database. The sequence will be saved in a file with the name of the database appended at the end of the name. For example, the sequence "hba_human" is saved in a file called "hba_human.swissprot" because "hba_human" comes from the Swissprot database.
cyrus% fetch hba_human <Return>Now, do the same for the rest of your sequences.
cyrus% toig *.swissprot <Return> ToIG converts GCG sequence file(s) into a single file in IntelliGenetics format. glb5petma 149 aa hbahorse 141 aa hbahuman 141 aa hbbhorse 146 aa hbbhuman 146 aa lgb2luplu 153 aa mygphyca 153 aa What should I call the output file (* glb5_petma.ig *) ? swiss.ig <Return> cyrus% dir *.ig <Return> 2 1coh.ig 2 2mhb.ig 136 swiss.ig cyrus% cat *.ig > peps <Return> cyrus% more peps cyrus% IG-to-tbl peps > peps.tbl <Return> cyrus% pima.sh <Return> Usage: pima.sh CLUSTER_NAME SCORE_CUTOFF seq_filename [REF_SEQ_NAME sec_struct_seq_file [ss_gap_penalty] ] cyrus% pima.sh hbhorse 25.0 peps.tbl <Return> Or, if you have secondary structure information to improve your alignment: cyrus%pima.sh hbhorse 25.0 peps.tbl 1ldm 1ldm.ss <Return>The pima program will create the following output files.
cyrus% dir hbhorse* <Return> cyrus% dir hbhorse* 2 hbhorse-ML.cluster 10 hbhorse-ML.pima 2 hbhorse-SB.pattern 10 hbhorse-ML.mase 2 hbhorse-SB.cluster 8 hbhorse-SB.pima 2 hbhorse-ML.pattern 10 hbhorse-SB.mase cyrus%The files "hbhorse-SB.pima" and "hbhorse-ML.pima" will contain the alignment information.
To put this alignment information into a prettier format, you can use the "print_pima.sh" program.
cyrus% print_pima.sh hbhorse-ML.pima > hbhorse-ML.pp <Return> . cyrus% more hbhorse-ML.pp <Return>You can align your set of protein sequences on our WWW site at http://bmerc-www.bu.edu/protein-seq/pimaII-new.html
You can access a comprehensive list of multiple alignment programs at the VSNS BioComputing Division Multiple Alignment Resource Page http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/welcome.html
You can learn more about multiple sequence alignments by going to the ALGORITHMS FOR MULTIPLE SEQUENCE ALIGNMENTS homepage at the www site http://ben.vub.ac.be/embnet.news/vol2_1/align.html