BFASTA/BTFASTA(1) OGMP SEQUENCE UTILITIES BFASTA/BTFASTA(1) NAME bfasta - perform fasta searches on multiple sequences in a library file btfasta - perform tfasta searches on multiple sequences in a library file SYNOPSIS bfasta/btfasta [-p] [-o outfile] [-a nb_align] [-s nb_scores] [-i] [-n nb_res] query_library target_library DESCRIPTION These programs have been written to circumvent the fact the the original fasta(1) and tfasta(1) search only the first sequence in a library file. With bfasta and btfasta, all the sequences contained in a library file can be searched interactively. Both programs are essentially identical except for the main engine used to perform the search on the individual sequences: bfasta uses fasta(1) and btfasta uses tfasta(1). If any of the two libraries passed on the command line is not in the current directory, bfasta/btfasta will try to see if it is in /research/Seqbanks, and use that library instead if it finds it. By default bfasta/btfasta will looks at 20 scores for each item in the query library and 20 alignments for each score. These values are configurable though (see OPTIONS). Bfasta will only retain the 500 best (according to the maximum "opt" score obtained) result sets. It is possible to modify this behavior though (see OPTIONS -n and -i). Note that if the two file argument "query_library" and "target_library" are textually the same (so they are the exact same file), bfasta will adjust its processing in order to NOT compare any sequence with itself. A way to bypass this mechanism is to use two copies of the same file, or use two different ways to specify the same file, e.g. bfasta file ./file OPTIONS -o outfile Put all the result in file outfile. If this switch is not used, all the results will go in to a file named bfasta.out (for bfasta) or btfasta.out (for btfasta). -p By default, every match that the program finds goes in the result file. With this option, the user will always be prompted before a particular result is written in the result file. -a nb_align Show nb_align alignments per score. If this option is not used, 10 alignments per score will be displayed. -s nb_scores Show nb_scores. If this option is not used, 20 scores will be displayed. -n nb_res Keep the best (according to the maximum "opt" score obtained, or the maximum "initn" score obtained) nb_res results instead of the set of results obtained for the whole query library. If this option is not used, the best 500 results are kept. -i To determine if a result is better than another, use the maximum "initn" score obtained during the fasta search instead of (the default) the maximum "opt" score. DEPENDENCIES /share/supported/apps/fasta/bin/fasta34 Used to search the sequences in the target library (for bfasta) /share/supported/apps/fasta/bin/fasta34 Used to search the sequences in the target library (for btfasta) SEE ALSO fasta3(1), btfasta(1) AUTHOR Gertraud Burger (specs and original shell script version) Nicolas Brossard (programming and manpage) Organelle Genome Megasequencing Project, APR 1998