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ClustalW and Omega of EBI and Blast of NCBI, both globally align sequences. Smith waterman of EBI aligns sequences locally, but works with just two sequences. How can I align more than 2 sequences locally?

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You have to do it pairwise (there is no other option).

You can do that with BLAST or even SSEARCH (Smith-Watermann). If you have a fasta file of your sequences then do this:

  • make index of your sequences using makeblastdb -dbtype nucl -in <yourfastafile> -out <yourdbindex>
  • Run BLAST with your <yourfastafile> as input and <yourdbindex> as database with desired parameters. This will do a pairwise alignment between all sequences

Similar strategy can be used for SSEARCH.

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  • $\begingroup$ I just use GUI based software and sites. what are these codes? $\endgroup$ – user11667 Mar 16 '15 at 8:41
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    $\begingroup$ @StackUnderFlow This is the command to run blast in commandline (UNIX terminal or Windows command prompt). blast does not have a GUI or even if there is one, I have never used it. It is much better to write commands (it saves RAM and also allows you some automation) $\endgroup$ – WYSIWYG Mar 16 '15 at 8:43
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    $\begingroup$ The various web-based BLAST tools are basically a GUI for BLAST. $\endgroup$ – terdon Mar 17 '15 at 17:23
  • $\begingroup$ @terdon Ohh yes that's true but they don't give much controls. $\endgroup$ – WYSIWYG Mar 17 '15 at 17:32
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    $\begingroup$ More than you might think. The NCBI blast lets you set things like e-value, gap penalty, match/mismatch scores, low complexity filtering. That's more than enough for 99% of uses. $\endgroup$ – terdon Mar 17 '15 at 17:43
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Even Water (in EBI itself) is Local alignment tool for multiple sequence alignment. Also in BLAST you get bla2seq which is also used for pairwise alignment. In any of these tools you just have to enter FASTA sequences (any number you want) or any sequence with > sign and run it against the subject (database or your required sequence). If you want to see the results for all the alignment in one screen, a tool like BioEdit would be ideal. I hope this is helpful, I'm not an expert in bioinformatics so feel free to correct me :)

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  • $\begingroup$ Thanks but those tools are for pairwise alignment but I need a multiple alignment tool which locally align sequences $\endgroup$ – user11667 Mar 15 '15 at 8:47
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I use Jalview, that is a small program written in Java. It is simple to use and can do many many things. It's web-service based and it has 7 different services built in just for sequence alignment. You can load your sequences from many file formats, or get them by reference id. It's really a small swiss-army-knife. I really recommend to take a look at it. It's available on http://www.jalview.org/.

EDIT:

I might have missed the local alignment part earlier, but I did some research and found that MULAN (MUltiple sequence Local AligNment and conservation visualization tool ) may be what you're looking for.

PMC article of Mulan, and the manual for Mulan.

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  • $\begingroup$ Thanks and where is Multiple local align in jalview? $\endgroup$ – user11667 Mar 15 '15 at 9:46
  • $\begingroup$ @StackUnderFlow Jalview may not have what you need but I edited my answer and found Mulan that might suit your needs. $\endgroup$ – Nandor Poka Mar 15 '15 at 10:19
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    $\begingroup$ jalview is not for local alignments. $\endgroup$ – WYSIWYG Mar 16 '15 at 8:38
  • $\begingroup$ Yes, I know that's why I edited my answer, but maybe I'll delete that part, so it won't be misleading. $\endgroup$ – Nandor Poka Mar 16 '15 at 9:07

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