System.out.println("Adding dbref to "+sequence[m].getName()+" : "+\r
entry.getAccession().elementAt(0).toString());\r
\r
- String nonGapped = AlignSeq.extractGaps("-. ", sequence[m].getSequence());\r
+ String nonGapped = AlignSeq.extractGaps("-. ", sequence[m].getSequence()).toUpperCase();\r
\r
int absStart = entry.getUniprotSequence().getContent().indexOf(\r
nonGapped.toString());\r