Is It Possible To Get Near Global Alignment From Blast?

Question

[Raghul]

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

[Niek De Klein]

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

Answer 1

[Istvan Albert]

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

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

[Raghul]

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

Answer 2

[Bill Pearson]

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/