Which Software Can Generate Local Alignment?
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9.5 years ago
sanchezcavani ▴ 220

Could anyone let me know which software I can use to do local alignment of two sequences? Thanks very much!

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9.5 years ago
Fred ▴ 780

Maybe you can start with "water" (implementation of Smith and Waterman local alignment) in the EMBOSS package.

In Unbuntu: apt-get install emboss!

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Thanks a lot! I should not forget Water! It is very famous!

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9.5 years ago
cts ★ 1.7k

wikipedia has a comprehensive list http://en.wikipedia.org/wiki/List_of_sequence_alignment_software

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Wikipedia's List of sequence alignment software page is far from comprehensive... but it does provide a reasonable selection of options to start with.

For example: the list is missing some of the EMBOSS alignment programs

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9.5 years ago

The below two pages list several options for aligning two reads.

http://www.molbiol-tools.ca/Alignments.htm

http://www.ebi.ac.uk/Tools/psa/

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Thanks so much!

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9.5 years ago
gammyknee ▴ 210

BLAST (ie. BLAST2SEQ)

http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=megaBlast&BLAST_SPEC=blast2seq

Edit: I second water too. Its very useful (albeit quite slow...)

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Thanks! I get it!

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6.8 years ago
Suzanne ▴ 100

Jalview is a free MSA visualisation software that can generate local alignment within large protein. It offer a range of multiple sequence alignment tools including Clustal Omega, Clustal W, Mafft, Muscle, Tcoffee and Probcons. They have YouTube video playlist about 'Selecting and Editing Sequences using Jalview'.

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