Online alignment for large fasta files

Question

[mkh]

Hi

I have a fasta genome file that contain 4000 genomic sequences (~ 30Mb size) in it. I would like to align this 4000 sequence to a reference genome. I was trying to use SINA (reference base multiple sequence alignment) in galaxy (https://usegalaxy.org/) however I have got memory error. Is there any online sources that I perhaps can use for this purpose?

Thanks,

[Fatima]

If you only need to align the sequences to a reference, I'd suggest blastn

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

You may also be able to use mummer: http://mummer.sourceforge.net/

If you have sequencing reads, you can use bowtie2.

Answer 1

[hugo.avila]

Hi, try CSAR web. Just upload a reference and you 4000 genomic sequences and you will get an mummer alignment, a fast scaffold and a dot plot. But i really recommend that you perform this type of analyses locally in order to get more control of your work.