Question: Online alignment for large fasta files
0
gravatar for mkh
29 days ago by
mkh40
USA/CT
mkh40 wrote:

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,

fasta sequence alignment genome • 132 views
ADD COMMENTlink modified 29 days ago by hugo.avila160 • written 29 days ago by mkh40

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.

ADD REPLYlink modified 29 days ago • written 29 days ago by Fatima820
0
gravatar for hugo.avila
29 days ago by
hugo.avila160
hugo.avila160 wrote:

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.

ADD COMMENTlink written 29 days ago by hugo.avila160
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