Hi all, I'm more on the computer than biological side, so excuse my ignorance on this, but you guys have been a big help in the past and hope someone can answer my question.
I have mpiblast running well on my system with a web interface that has the basic Blast template that comes with NCBI's wwwblast. A user of mine asked me if there was a way I can limit by entrez/organism as seen on the NCBI version's web interface for Blast near the bottom of the page: http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?CMD=Web&LAYOUT=TwoWindows&AU TO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwise&CLIENT=web&DATA BASE=nr&DESCRIPTIONS=100&ENTREZ_QUERY=%28none%29&EXPECT=10&FILTER=L&FORM AT_OBJECT=Alignment&FORMAT_TYPE=HTML&GENETIC_CODE=1&NCBI_GI=on&PAGE=Tran slations&PROGRAM=tblastx&SERVICE=plain&SET_DEFAULTS.x=21&SET_DEFAULTS.y= 9&SHOW_OVERVIEW=on&UNGAPPED_ALIGNMENT=yes&END_OF_HTTPGET=Yes&SHOW_LINKOU T=yes Does mpiblast have a flag or some kind of option for me to do this? Do databases have to be formatted in a specific way to enable this? Or does NCBI just BLAST against everything, and then based on your limiting run some kind of script or finalizing function to parse out the appropriate stuff you want? This would be the easy way, but efficiency and speed would be the problem here because of the wasted computation cycles on stuff the user doesn't need. I'm guessing this is probably not their approach. Any ideas or advice would be helpful in implementing this option, no matter how tedious or difficult. Thank you very much, Ray Chan Plant Sciences BioComputing Center Univ. of Calif, Davis ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid0944&bid$1720&dat1642 _______________________________________________ Mpiblast-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mpiblast-users
