Aligning two DNA sequences with nBLAST

Question

[sj93]

Because I am so new to DNA sequencing and this type of software, I likely do not have the terminology to explain my question properly. I will post the three files I refer to and hopefully that will make my question more clear.

I have two fasta files containing different genomic sequences of the american eel. I have other data (mergedTables) that correspond to one of the two versions (GCA_001606085.1_ASM160608v1_genomic) of the american eel genome that I have. I would like to use the other version (american_eel_genome_v5), as I have an annotation file that I can use with it in IGB. I've been told that I can use the BLAST algorithm to solve my problem, but I do not understand how as I thought blast was used to find similarities in different species.

Any suggestions would be really helpful. I'm an undergrad working on an independent study.

[GenoMax]

Aligning chromosome sized pieces is not the best use for BLAST since it does local alignments. You should look into LASTZ (https://github.com/lastz/lastz ) for this type of an application.

[sj93]

Thanks genomax. From what I can tell, LASTZ seems to require some knowledge of coding/running source code, which I am completely unfamiliar with. Is this program intended for use for people with more advanced skills?

[GenoMax]

If you have managed to run a blastn search on the command line (Can I align two DNA sequences using BLAST from command line? ) then you may be able to use LASTZ. You can find the precompiled binaries for linux on this page: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/

It is would not be an easy program to use. You may want to find a local collaborator who can assist with this task.

Answer 1

[pltbiotech_tkarthi]

You can try: http://genome.lbl.gov/cgi-bin/VistaInput?alignac_pgm=lagan&num_seqs=2 or try https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&LINK_LOC=align2seq or Clustal Omega https://www.ebi.ac.uk/Tools/msa/clustalo/. You must use fasta format sequence. Better you can try LAGAN alignment from the above link, LAGAN does Global Alignment. Read this article about genome alignment: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430158/ Also try this: A: How to analysis mutations effects bioinformatically?

[sj93]

Thanks for the suggestions! I had tried ncbi blast before posting this question, but It would just load forever then give me an error message. I'm trying the vista input link you sent, but I think I'm going to get the same result. The files I am trying to use are 1.4 GB, and I noticed that Clustal Omega aligns a file with a max size of 4 MB. Do you know if the first two links you suggested should be able to handle that size?

Answer 2

[pltbiotech_tkarthi]

Also LAGAN will align the sequences with maximum size limit of 10MB. So please try the LASTZ as suggested by Genomax. Besides, you could try BLAST+ https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download this is Linux based. See this http://pipeline.lbl.gov/methods.shtml for genome alignment and read this as well http://pipeline.lbl.gov/vgb2help.shtml