[Biojava-l] Impossible to catch Location parsing Error

Hello, everyone. I mail BioJava-ML for the first time. I'm trying to parse DDBJ Format data, which is similar to GenBank-Format. The problem arose. DDBJ's data contain illegal? Location of Feature, so the number of start position is greater than that of end position, for example, "92619..88345".

Re: [Biojava-l] Impossible to catch Location parsing Error

Hi Hiroyuki, The genbank parser was not designed with DDBJ in mind, so I am not supprised that it fails. I am suprised that you have feataures with backwards coordinates - I thought that genbank, embl and DDBJ had agreed to use the exact same feature table format, but I may be wrong here. Do you

[Biojava-l] Question about cutting a sequence

I've had these questions since I started using Biojava a year ago, and I still can't get it right: 1. How can I take a certain part of an annotated sequence (let's say from bp 500 to 750), make a new sequence from this part, while retaining all annotations of the piece, in new coordinates? So a

Re: [Biojava-l] Question about cutting a sequence

On Fri, Sep 20, 2002 at 03:18:07PM +0200, Stein Aerts wrote: > > I've had these questions since I started using Biojava a year ago, and I > still can't get it right: > > 1. How can I take a certain part of an annotated sequence (let's say from bp > 500 to 750), make a new sequence from this part