Lets say I want to do pairwise alignments of 2 sequences. How can I do this?
Look at Bio::Factory::EMBOSS to see how to use the ‘water’ and ‘needle’ alignment programs that are part of the EMBOSS suite. Additionally you can use the pSW module that is part of the bioperl-ext package (distributed separated at ftp://bioperl.org/pub/DIST). However note this only does protein alignments and is no longer a supported module. Instead the EMBOSS implementation is the the best path ahead unless someone else wants to provide an Inline::C implementation.
Look at Bio::Factory::EMBOSS to see how to use the ‘water’ and ‘needle’ alignment programs that are part of the EMBOSS suite. Bio::Factory::EMBOSS is part of the bioperl-run package. Or you can use the pSW module for DNA alignments or the dpAlign module for protein alignments. These are part of the bioperl-ext package (distributed separated at ftp://bioperl.org/pub/DIST). Q3.5: I’m using Bio::Search* and its frame() to parse Blast but I’m seeing 0, 1, or 2 instead of the expected -3, -2, -1, +1, +2, +3. Why am I seeing these different numbers and how do I get the frame according to Blast? A: These are GFF frames – so +1 is 0 in GFF, -3 will be encoded with a frame of 2 with the strand being set to -1 (for more on GFF see http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml).
