FW: Help with ShortBRED : Sam Davison

[Levesque, Nicole M.]

 

Good afternoon – please see below.

Thanks

Nicole

 

From: Samuel A Davison <sdav...@purdue.edu>
Sent: Tuesday, July 31, 2018 9:56 PM
To: Levesque, Nicole M. <leve...@hsph.harvard.edu>
Subject: Help with ShortBRED : Sam Davison

 

Dear Dr. Levesque,

 

My name is Samuel Davison and I work under Dr. Sharma and Dr. Gomez of the University of Minnesota: Twin Cities. We wish to use shortBRED for our research but have ran into some issues with the program not recognizing where cd-hit is and believes muscle is not giving a valid output. We have attempted to rename cd-hit to the name that is recommended to no avail. Also, it would be very much appreciated if you could explain how shortBred uses usearch, muscle, cd-hit and blastp are used or what components of them are used by shortBRED.

 

Thank you for your consideration,

 

Sincerely,

 

Samuel Davison

[Eric Franzosa]

Hi Samuel,

Sorry for the delayed reply - is it possible to include the specific error messages that you're seeing? That will help us to diagnose and solve the problems that you're seeing. In answer to your question about the specific software binaries:

ShortBRED-Identify uses CD-HIT to cluster input proteins-of-interest into families. We then use MUSCLE to build a consensus sequence for each family. Finally, blastp compares the consensus sequences to one another and a background protein "universe" to weed out non-unique subsequences from the proteins of interest. The remaining unique sequences (or minimally non-unique sequences) are then used as markers for those proteins. ShortBRED-Quantify then uses USEARCH to map sequencing reads to the markers to quantify their corresponding proteins from a metagenome or metatranscriptome.

Thanks,

Eric

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