BlastAlign Web Interface - Version 1.0

BlastAlign: a program that uses blast to align nucleotide sequences that have large indels (INsertions/DELetions) or are otherwise difficult to align.

BlastAlign uses the NCBI Blast program to make the alignment.

Some important points to remember:
  • The output is an alignment of all other sequences to the one 'most representative' sequence
  • Regions that are not present in this 'most representative' sequence will not be recovered
  • The more variable regions may also not be recovered (and hence it will appear that they have been cut out of the output)
  • The 'Advanced options' link allows you to modify the way BlastAlign works, e.g. to choose the 'most representative' sequence, or to exclude the more 'gappy' sequences
There are many multiple alignment programs available on the web. We wrote BlastAlign to find alignments from difficult sequence files that more sophisticated alignment programs are not intended to cope with, e.g. where the sequences have large indels, or some sequences are not homologous to the others.

The speed and robustness of BlastAlign also make it useful for preliminary data analysis.

Go to the BlastAlign web interface page.

Web-interface developed by Aris Katzourakis, Robert Belshaw and Tulio de Oliveira.

Page last updated by Tulio de Oliveira.