Orthomclblastparser Problems In Orthomcl Programs

Question

[wang.qiang.prc]

Hi,

Today I use OrthoMCL to find orthology. When I go on the orthomclBlastParser, I find a problem that can not resolve my_blast_results_in_tab_format.Please give me a little advice~~Thank you@@

Problems:

$./orthomclBlastParser my_blast_results my_orthomcl_dir/compliantFasta >> my_orthomcl_dir/similarSequences.txt
acquiring genes from all_VS_all.out.tab

             'all_VS_all.out.tab' is not in 'taxon.fasta' format-------------------------------------->why? where is wrong?

[Damian Kao]

Did you format your fasta files so the header is in the format orthomcl wants?

[wang.qiang.prc]

Could you please speak in detail? You mean I should format the blast results in order to normalize the file??????? Many Thanks~~

[Damian Kao]

Did you run all the previous steps in orthomcl? Did you run the orthomclAdjustFasta and orthomclFilterFasta scripts? Do the fasta headers all have proper ids?

[wang.qiang.prc]

yes, I have run the orthomclAdjustFasta and orthomclFilterFasta. These are all successful. But I do not understand the proper ids and the fasta headers you said. Explain it?

[anna.kostikova]

I think you have a file called all_VS_all.out.tab in your my_orthomcl_dir/compliantFasta folder. Check this folder to ensure that there are only well-formatted fasta files in there.

Also, would like to link my tutorial about usage of OrthoMCL - maybe it will be helpful.

Answer 1

[Neilfws]

Examination of the Perl code reveals this line:

$fastaFile =~ /(\w+).fasta/ || die "'$fastaFile' is not in 'taxon.fasta' format\n";

This indicates that the program expects a Fasta file with a name ending in ".fasta". It seems that all_VS_all.out.tab is not such a file.

[wang.qiang.prc]

I found my m8 format blast result is just like this:

ay|AYWB_001    1_goodProteins.fasta    100.00    504    0    0    1    504    1    504    0.0     991
ay|AYWB_001    672_goodProteins.fasta    91.72    507    39    1    1    504    1    507    0.0     907
ay|AYWB_001    1379_goodProteins.fasta    22.11    285    171    9    201    466    13    265    0.008    33.5
................

I think the second colum is wrong. How do I make it correct?????

3q++Regards~~

Answer 2

[Md]

if you run this command, you have a correct selfblast file.

makeblastdb -in goodProteins.fasta -dbtype prot -title selfblast -parse_seqids -out selfblast -logfile selfblast.log
blastp -db selfblast -query goodProteins.fasta -seg yes -out selfblast.out -evalue 1e-5 -outfmt 7 -num_threads 24