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how to locate genes coding on the reference genome

Hello Biostar,

I work on 6 genomes of the same species (Funji) and for each sample, I have three multifasta files containing coding genes (CDS) involved in pathogenicity.

Could you offer me a tool that would allow me to locate these genes on the chromosomes of the reference genome. My goal is to locate the distribution of these genes from each sample on the reference genome.

Thank you in advance.

localization alignment sequence software genome
• 2,019 views • link
updated by Nicolas Rosewick Nicolas Rosewick • written by kamel • kamel

Like a classic aligner BWA/Bowtie2 or do you want to align your sequences on the 6 genomes at once ?

• 1 views • link
written by Bastien Hervé Bastien Hervé

Yes, I want to locate my sequences of these 6 samples (3 multifasta per sample) on the reference genome at once.

• 1 views • link
written by kamel • kamel

1 answer

gmap handles well cDNA mapping on genomes : http://research-pub.gene.com/gmap/ and https://github.com/juliangehring/GMAP-GSNAP for examples

• 1 views • link
written by Nicolas Rosewick Nicolas Rosewick

I will use it and I will come back to you. Thank you

• 1 views • link
written by kamel • kamel

Thank you gmap is more convenient in this case. now I have the positions of my sequences on the reference sequence. I just posted a question to see how I could graphically represent these positions on the chromosomes. Do you have an idea?

• 0 views • link
written by kamel • kamel

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