Sequences number of Orthomcl results (groups.txt) were lower than raw data (fasta file) · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

Sequences number of Orthomcl results (groups.txt) were lower than raw data (fasta file)

Hello everyone!

I tried to cluster 10000 protein sequences through Orthomcl, while my Orthomcl results (groups.txt, the output file of orthomclMclToGroups) only contained 6853 sequences. Is it suitable? I thought the mismatch may be for unsuitable blast tool were used, so I want to know which blast tool commonly used in orthomcl analyses, blast2 or blast+?

Thanks

orthomcl

• 2,518 views • link

updated 3.8 years ago by Ram

• written 11.0 years ago by Ginsea Chen

1 answer

I'm not 100% sure but I believe that OrthoMCL doesn't output singletons at the pairs and groups stage of the analysis. I would suspect that that is what makes up the bulk of your missing values. You could check this by looking at the BLAST results for sequences that didn't make it to the output stage and see what their BLAST scores/hits look like.

• 0 views • link

written 11.0 years ago by DG

Log in to answer this question.

More posts like this

reciprocal BLAST meaning
written 10.2 years ago by anuj2054 •

I am Anuj, a PhD student, from the University of Oklahoma. I was trying to replicate your PNAS paper titled : " Major diversification of …
Too many sequences of EVM output
written 10.7 years ago by Ginsea Chen

<p>Dear all.</p> <p>I used EVM to intergate all evidences (de novo, RNA-seq and protein evidences) into a single gff3 file (evm.out.gff3), and then found that …
I want to annotate special regions (which were hit region of a gene family sequences) of genome
written 10.7 years ago by Ginsea Chen

Dear all I have a interested gene A which sequence information have been cloned and expression patterns have been analyzed in species A, while I …
BLAST step of GO enrichment analyses
written 10.9 years ago by Ginsea Chen

Dear all! I used nr database which download from NCBI as query database in BLAST step of GO analyses, and then I loaded this result …
Low DE gene numbers after Trinity analysis
written 11.0 years ago by Ginsea Chen

Dear all! I tried to use trinity to assemble my RNA-seq raw data and find some differential expression genes between control and experiment groups. Two …
Multiple Alignment of several homologous gene
written 11.1 years ago by kaihami •

<p>Hello everyone,</p> <p>My very first Biostar question here. I'm new in bioinformatics, so sorry if my questions are very naive...</p> <p>I'm trying to align a …
special region annotation of plant genome
written 11.5 years ago by Ginsea Chen

<p>Hello everyone.</p> <p>I tried to annotate a plant genome though maker, while I have no time to wait the results because of Spring Festival coming. …
Problems about gene family identification and characterization
written 11.9 years ago by Ginsea Chen

Hello everyone I tried to use some known sequences as query database to search whole members of special gene family in whole genome database through …
Blast Is Giving Me A Result Totally Unrelated To The Gene I Expect
written 13.3 years ago by r.a.konrad •

<p>Hello,</p> <p>After I obtained the results from sequencing, I proceeded to curate the sequences and identifying (with Vector NTI) the primers I used in the …
Protein Functional Annotations
written 13.5 years ago by Rahul Sharma

<p>Dear all,</p> <p>I have predicted genes (both homology and ab-initio based methods were used) after the genome assembly of a fungal genome. Using OrthoMCL, orthologs …