Question

Alignment of genomic data

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7.7 years ago

mittu1602 ▴ 200

Hello, I have fungi genome sequenced data in FASTA format which is 20mb in size and I want to align my data with Diaporthe ampelina which is 40mb in size. I am looking for a tool apart from BLAST. I have already tried YASS tool but it does not work with such large data, it does work finely with small data, I am looking for similar type of tool which can work with my large data.

Thank you, Meetali

blast sequence genome • 1.5k views

ADD COMMENT • link updated 7.7 years ago by Felix Francis ▴ 600 • written 7.7 years ago by mittu1602 ▴ 200

score 5 · Answer 1 · 2017-03-09

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7.7 years ago

Felix Francis ▴ 600

MUMmer: http://mummer.sourceforge.net/manual/

LAST: http://last.cbrc.jp/

mugsy: http://mugsy.sourceforge.net/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3031037/

ADD COMMENT • link 7.7 years ago by Felix Francis ▴ 600

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Thank you Felix,

MUMmer worked too well for my work.

ADD REPLY • link 7.7 years ago by mittu1602 ▴ 200

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If an answer is helpful, upvote it. If the answer resolved your question, mark it as accepted.

ADD REPLY • link 7.7 years ago by WouterDeCoster 47k

score 1 · Answer 2 · 2017-03-09

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7.7 years ago

Pierre Lindenbaum 164k

try LASTZ ? https://www.bx.psu.edu/~rsharris/lastz/

ADD COMMENT • link 7.7 years ago by Pierre Lindenbaum 164k

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Hello, Pierre LASTZ worked too but the result files were not well interpreted, Thank you.

ADD REPLY • link 7.7 years ago by mittu1602 ▴ 200