AHA is a package for creating sequence analysis pipelines that end in an ACEDB
instance. In its simplest form, I use it to browse a FASTA file in ACEDB. This
alone is pretty useful. One of my mantras is "don't use an editor to view
sequences". But I also use AHA to drive complex pipelines that involve
RepeatMasker, WU-BLAST, Genscan, etc.
How does it work?A sequence analysis pipeline is not much different from compiling a bunch of inter-dependent sources. In this spirit, AHA is driven by the unix make utility. There are several Perl scripts that do most of the post-processing to format the data into gff and ace files. The ace files are then loaded into ACEDB along with the sequences, including (optionally) the homologies if you've run BLAST. This lets you take your ACEDB offline and browse at your convenience. I do this on a laptop while I watch cartoons with my daughter.InstallationInstalling AHA is not too complicated, but it does require some hand-editing to set up paths for your local environment. Creating new analysis types is also not too complicated, but you must make sure your dependancies are logical.Release NotesThis is unsupported, free software. If it doesn't meet your needs, don't use it. Please report bugs, but don't expect me to fix them immediately (if at all).gbace.plgbace.pl is a related piece of software. It turns GenBank documents into ACEDB instances. This is really rough work, but it works well enough to be useful. In particular, the display methods are not at all complete. Going through the DDJB/EMBL/GenBank Feature Table description and assigning colors and priorities would fill this out, but it is not high on my priority list. |
Download the tarball Download gbace tarball
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