how to locate genes coding on the reference genome

Question

[kamel]

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.

[Bastien Hervé]

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

[kamel]

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

Answer 1

[Nicolas Rosewick]

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

[kamel]

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

[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?

[Nicolas Rosewick]

check the karyoploter package in R : https://bioconductor.org/packages/release/bioc/html/karyoploteR.html and search also within biostars