Which Software Can Generate Local Alignment?

Question

[sanchezcavani]

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

Answer 1

[Fred]

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

In Unbuntu: apt-get install emboss!

[sanchezcavani]

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

Answer 2

[cts]

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

[Hamish]

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

Answer 3

[Ashutosh Pandey]

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/

[sanchezcavani]

Thanks so much!

Answer 4

[gammyknee]

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...)

[sanchezcavani]

Thanks! I get it!

Answer 5

[Suzanne]

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'.