[Biojava-l] Masked regions, X's, No Call's N's

[Matthew Pocock]

Hi Kevin,

Which version of BioJava are you working from? Could you check that you
either have the 1.01 release, or a fresh check-out from the anonymous CVS
repository. It is probably best to grab the source code release as it has
some demos included:

http://biojava.org/download/source/biojava-1.01.zip

N characters should appear in the DNA alphabet as ambiguity symbols, so you
should be fine parsing them. I don't think that X is in there - what does X
represent? Could you try running the demo called:

symbol.TestAmbiguity

You need to have build biojava, and have biojava.jar and xerces.jar in your
classpath, and then cd into the demos directory and type:

java symbol.TestAmbiguity

This should print out a list of lines something like:

adenine -> {adenine}
guanine -> {guanine}
cytosine -> {cytosine}
thymine -> {thymine}
ag -> {adenine, guanine}
ct -> {thymine, cytosine}
ac -> {adenine, cytosine}
GT -> {thymine, guanine}
gc -> {cytosine, guanine}
at -> {thymine, adenine}
act -> {thymine, adenine, cytosine}
gtc -> {thymine, cytosine, guanine}
gac -> {adenine, cytosine, guanine}
gat -> {thymine, adenine, guanine}
agct -> {thymine, adenine, cytosine, guanine}
gap -> {}

If none of this helps, then mail the list and/or me, and we will see if we
can get you up-and-running.

Matthew

"Kevin T. Pedretti" wrote:

> Hello All,
>   I'm just starting to use biojava and have already hit a roadblock.  The
> DNA alphabet doesn't contain symbols for X's or N's so when I try to read
> in a fasta sequence with these characters, it throws a bunch of
> exceptions. Can I extend the alphabet to contain these characters and
> expect everything else to still work.  Sorry if this has been covered
> before and thanks for your help.
>
> Kevin
>
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