Question: Finding gene matches using sequence reads?
0
gravatar for anabaena
4 days ago by
anabaena0
anabaena0 wrote:

Hey all, I am looking through large data sets to try and find a gene cluster or particular genes using sequence reads. The goal is to find a metagenomic set with the genes of interest, essentially just a probe to see if what I am looking for is there. Currently, I am using Bowtie2 but I was wondering if there were any other ways to go about this? And if Bowtie2 is the best option, are there particular parameters I should consider/set when doing the alignment?

Thanks!

metagenomic bowtie2 reads • 87 views
ADD COMMENTlink modified 3 days ago by Fatima340 • written 4 days ago by anabaena0
1

It might be a good idea to assemble the reads and use a tool like Fraggenescan (it's really fast) to predict the gene sequences and then you can use blast to search them against your genes of interest.

The following pipeline might give you some ideas:

https://experiments.springernature.com/articles/10.1007/978-1-4939-7015-5_3

ADD REPLYlink modified 4 days ago • written 4 days ago by Fatima340

Awesome! So my main concern is that I have many samples to look through. The initial thought was to probe a metagenomic sample/read set and look for the gene of interest, and if present then go in an assemble reads and give the sample a deeper look. So with that being said would this pipeline be efficient in doing this?

ADD REPLYlink written 4 days ago by anabaena0

You don't need to use the whole pipeline (Fun4me) . You can just use Fraggenescan to predict the gene sequences and then use blast.

Please see the last line of this link (examples of Fraggenescan results using metagenomes as input):

https://omics.informatics.indiana.edu/FragGeneScan/result.php

I haven't seen your data so I'm not sure what's the best approach.

ADD REPLYlink modified 3 days ago • written 3 days ago by Fatima340
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1167 users visited in the last hour