Need help with sequence similarity networks programmes

Question

[talk4torypam]

Hi all,

I am trying to find similarity networks within my sequences and I have found 3 programs available for use

1. fusedTriplets
2. mosaic finder
3. Composite search

I have tried to use them (anyone of them will do) but for each one I encounter problems. With fusedTriplets I always get the error Assertion error: network header should start with 'qseqid sseqid', although I have tried different blastp outfmt (6, 7, 10) options. With mosaicfinder and CompositeSearch, I am unable to get to the execution path.

Please, I need help. Thank you

[Sej Modha]

Please provide more information about the problem you're facing here by including details about sample input file(s), type of computer system you're working on etc and please spare a few minutes to read How To Ask Good Questions On Technical And Scientific Forums

[talk4torypam]

hi, I am using linux command line to run these applications 1) For fusedTriplets.py the input file needs headers. I have used the following command lines to make the input file

makeblastdb -in all.fas -dbtype prot -title all -out allseqs -parse_seqids

And for the input file I used

blastp -query all.fas -db allseqs -out all-vs-all_dbsize_defult.tsv -outfmt 6
blastp -query all.fas -db allseqs -out all-vs-all_dbsize_defult.tsv -outfmt “6 qseqid sseqid evalue pident bitscore qstart qend qlen sstart send slen”

and I get the error Assertion error: network header should start with 'qseqid sseqid' I have tried using blast outfmt 7 (edited it too) and 10. 2) For mosaicFinder and Composite search I have installed all the dependencies but I cannot find the path to input my data

thank you

[Sej Modha]

Hi There,

I have never used any of these programs before, however, the error for fusedTriplets.py states that it needs the BLAST output headers in the file. You could try to run blastp with -outfmt 7 as it should include the header line for hits.