GENESEQ, USGENE, PATGENE: Combined Alignment Displays

The search results originated from a BLAST- or FASTA (GETSIM)-search and a GETSEQ-search may be combined in one L-number. With the command D ALIGNC a combined alignment display is provided in the databases GENESEQ, USGENE, and PATGENE which supports the quick evaluation of short sequence stretches within a longer sequence.

1. Run the BLAST- search.
   
   
   
   
2. Run the GETSEQ- search.
   
   
   
   
3. Combine the two results with AND.
   
   
   
   
4. Use D ALIGNC for the display.
   
   Displayed are the usual values from the BLAST-search and within the BLAST-alignment the GETSEQ-alignment with the double underlining and the L-number of the GETSEQ-search.
   
   

ALIGNC- Display for the Evaluation of Combined Search for CDR- and Antibody Sequences

The ALIGNC display may be used for the evaluation of the alignments after a search for Complementarity-determining regions (CDR) with GETSEQ and a search for antibody sequences using the BLAST- or FASTA- (GETSIM) algorithm which have been combined in one L-number.

1. Run the GETSEQ- searches for each CDR.
   
   
   
   and concatenate the results with AND
   
   
   
   
2. Run the BLAST- search with the maximum of results using the -MAXSEQ parameter.
   
   
3. Use high Score and Ident values.
   
   
   
   
4. Combine the GETSEQ- and BLAST- search with AND results into one L-number.
   
   
   In the combined display after D ALIGNC, each retrieved CDR is represented by the respective L-number and the short alignment from the GETSEQ- search within the alignment from the BLAST- search.