Is It Possible To Get Near Global Alignment From Blast?
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12.1 years ago
Raghul ▴ 200

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 • 7.8k views
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I'm unable to understand what you're trying to ask.

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12.1 years ago

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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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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12.1 years ago
Bill Pearson ★ 1.0k

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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