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Is It Possible To Get Near Global Alignment From Blast?

Hi to all When a query sequence identical to a database sequence is done BLAST, the alignment is shown for 100% of the sequence ie.complete coverage. Cannot this situation may be said global alignment? So when a query sequence is done database searching, does appropriate alteration of input parameters will ensure high coverage of sequence so that it shows alignment for maximum possible region?

thanks raghul

blast alignment
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updated by Bill Pearson Bill Pearson • written by Raghul Raghul

I'm unable to understand what you're trying to ask.

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written by Niek De Klein Niek De Klein

3 answers

Make sure to understand the differences between global and local alignments.

Keep in mind is that BLAST stands for Basic Local Alignment Search Tool

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written by Istvan Albert Istvan Albert

This is what I wanted to know "With sufficiently similar sequences, there is no difference between local and global alignments". thanks for the reply

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written by Raghul Raghul

The ggsearch36 program in the FASTA package will give you a true global alignment, and if you use the -m BB, -m 8, or -m 8C options, it will look like BLAST output.

Because requires sequences to be similar in length and uses SSE2 acceleration, it is also pretty fast.

ggsearch36 is available from: http://faculty.virginia.edu/wrpearson/fasta/fasta36/

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written by Bill Pearson Bill Pearson

The local alignment is the optimal substring of the global alignment. That's not an observation - it's actually the definition of a local alignment.

In other words, the local alignment is always contained within (or identical to) the global alignment.

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written by Jeremy Leipzig Jeremy Leipzig

This is not accurate. The optimal local alignment, may and often is, completely different than the optimal global alignment. As a simple example consider the sequences "ABCDEF" and "DEFGHI", and let the penalty for an indel be very large, say 10x that for a substitution. The optimal global alignment will contain 6 substitutions and no indels nor matches. While the optimal local alignment will contain just 3 matches, ie. "DEF".

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written by David R. Powell • David R. Powell

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