Figure 3

Blast servlet form and corresponding output. A FASTA formatted sRNA sequences can be inserted into the query box. Also target genomes or sRNAs have to be selected for multiple alignment using BLAST. For a detailed BLAST analysis the BLAST output analysis (BOA) options has to be selected. In this example four sRNAs resulting from a search with parameters shown in Figure 1 were selected as input. Genomes of the genus Listeria were set as targets and the BOA options were enabled. B The number of sRNAs detected in the target organism is displayed in a comparative matrix form. C All hits listed in a table and are linked to their corresponding alignment. D A detailed BLAST alignment of all results can also be plotted.