no_blast(1) OGMP SEQUENCE UTILITIES no_blast(1) NAME no_blast - run bblast on selected orfs in a masterfile SYNOPSIS no_blast [-g gcode] [-l length] [-F num] [-o ocode] [-L local_db] masterfile output_dir DESCRIPTION No_blast is a script used to perform blast searches on selected orfs in a masterfile. The ocode must only be given on the command line if the masterfile's name is not in genome_names.lst. The output_dir indicates where the bblast results will be written. No_blast performs the following actions: 1) Use mf2stad(1) to produce a coordinates file of all the genes in the masterfile, except the Vars, Sigs, Mots and Mobs. Be sure to use -o if the masterfile is not listed in genome_name.lst (see FILES). 2) Run flip to produce a prot.lst of all the orfs in the masterfile that have a length (without the stop codon) of at least 48. If -g was no used (see OPTIONS) no_blast looks in genome_name.lst (see FILES) to get the genetic code number. If it finds one, it runs flip with the option -g . Otherwise, flip is run without the -g switch (see flip's(1) manpage for a description of its behaviour in this case). 3) Use protfilt to filter the orfs: separate those for which there is at least one gene in the coordinates file that overlaps the orf by a given percentage (see -F) from those for which there is not. This will create the files prot.lst.nonoverlap and prot.lst.overlap in the current directory. 4) Run bblast on the orfs listed in prot.lst.nonoverlap and put the results in the output_dir passed on the command line. By default, bblast connects to NCBI to perform the blast searches. It is possible to have bblast search a local database instead (see OPTIONS). No_blast produces no output on stdout. All the output goes into the logfile no_blast.log, in the current directory. Upon completion, no_blast will ring the bell three times. It will also send a mail to the user indicating how the no_blast process terminated (success or failure). The bblast report can always be found in /REPORT OPTIONS -o ocode Use ocode as the organism code to use when running mf2stad(1). This option must be used if the masterfile is not listed in genome_name.lst (see FILES). -g gcode Pass the option "-g gcode" to flip. Gcode must be a positive number not greater than 21 and not equal to 7 or 8. If -g is not used, no_blast looks in genome_name.lst (see FILES) to get the genetic code number. If it finds one, it runs flip with the option -g . Otherwise, flip is run without the -g switch (see flip's(1) manpage for a description of its behaviour in this case). -l length When running flip, pass the option -l length. By default flip is run with -l48. -F num When running protfilt, pass the option -F%o-100. By default protfilt is run with the option -F%o20-100 -L local_db Instead of connecting to NCBI to perform the blast searches (the default), use the specified local database local_db instead. FILES no_blast.log The no_blast standard logfile /share/supported/apps/ogmp/lib/genome_names.lst Contains information on all the OGMP projects DEPENDENCIES /share/supported/apps/ogmp/bin/mf2stad To create the coordinates file /share/supported/apps/ogmp/bin/flip To produce prot.lst /share/supported/apps/ogmp/bin/protfilt To produce prot.lst.nonoverlap and prot.lst.overlap /share/supported/apps/ogmp/bin/bblast /usr/ucd/mail SEE ALSO mf2stad(1), bblast(1), protfilt(1), mail(1), flip(1) AUTHOR Gertraud Burger (specs) Nicolas Brossard (design and programming) Organelle Genome Megasequencing Project, Sept. 1998