Hendrik, experienced the same problem. We wrote some scripts to overcome this problem. Basically what we do is the following: 1 ) When you have a comparable "reference" genome we determine the synteny of the contigs by a blat analysis to the reference genome. From that we determine the possible contig order and strand orientation (normal or rev_compl). 2) The contig order + orientation list we use to join the contigs spaced by easily recognisable linkers (stretch of Ns and all START/STOPs in all frames to allow run-on and run-off ORF detection). In addition we write out a tab/embl feature file containing the contuig layout info. 3a) we either do an ORF detection using genemarkHMM and BLAST anlayse the results (again writing out the ORF annotation to an embl feature file) as wel as the first hits of the blast (but the latter is not really necesarry)). 3b) we perform a direct blast of the joined sequence and read in the blast results. Just my 5 cents... Alex
________________________________ Van: artemis-users-boun...@sanger.ac.uk namens Henrik Lantz Verzonden: do 29-4-2010 9:09 Aan: artemis-users@sanger.ac.uk Onderwerp: [Artemis-users] Multiple contigs and Blastall-results I was hoping I could get some help with a newbie Artemis question. Very new to all this. I have made a denovo assembly of a fungus using MIRA and 454-data only. The resulting fasta file with around 4000 contigs loads into Artemis fine. I can check all the contigs, find ORFs etc. The problem appears when I want to import the results of a blastall search on the contig-datafile. All annotations from the blastall results are lumped into the first five contigs, with the overwhelming majority in the first contig. Obviously not correct. I am using the -m 8 flag for the blastall search. Looking through the resultfile from blastall in a text editor I can see that the blastall search has worked, and there are many interesting hits, but I would like to visualize the results on the contigs. I read through the mail archive and found a user with a similar problem (http://www.mail-archive.com/artemis-users%40sanger.ac.uk/msg00463.html) and it seems one solution might be to save the contigs as a long continuous file in Artemis, and then use that in the Blastall search. But when I try that I get an error message from blastall: blastall(33748) malloc: *** mmap(size=1048576) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Bus error I am running on MacOSX Snow Leopard with 20 GBs of memory. Any help to get an inexperienced user started would be very much appreciated! /Henrik _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
