diff tools/blast_rbh/blast_rbh.xml @ 4:57245c11b8cb draft

Uploaded v0.1.0d, TBLASTX support; changed output columns

--- a/tools/blast_rbh/blast_rbh.xml	Fri May 16 11:16:02 2014 -0400
+++ b/tools/blast_rbh/blast_rbh.xml	Mon May 19 13:39:55 2014 -0400
@@ -43,6 +43,7 @@
                     <option value="blastn">blastn - Traditional BLASTN requiring an exact match of 11, for somewhat similar sequences</option>
                     <option value="blastn-short">blastn-short - BLASTN program optimized for sequences shorter than 50 bases</option>
                     <option value="dc-megablast">dc-megablast - Discontiguous megablast used to find more distant (e.g., interspecies) sequences</option>
+                    <option value="tblastx">tblastx - TBLASTX program using translated query against translated database (protein level matches)</option>
                 </param>
             </when>
         </conditional>
@@ -131,16 +132,16 @@
 ------ ---------------------------------
      1 ID from *species A*
      2 ID from *species B*
-     3 Bitscore from *A vs B*
-     4 Percentage identity from *A vs B*
+     3 Bitscore
+     4 Percentage identity
      5 Query coverage from *A vs B*
-     6 Bitscore from *B vs A*
-     7 Percentage identity from *B vs A*
-     8 Query coverage from *B vs A*
+     6 Query coverage from *B vs A*
 ====== =================================
 
 These values correspond to the ``bitscore``, ``pident`` and ``qcovhsp``
-values in the BLAST+ tabular output.
+values in the BLAST+ tabular output. For the bitscore and percentage identity
+the values for *A vs B* and *B vs A* are typically the same, so their minimum
+is shown. The coverage values differ according to the query lengths.
 
 .. class:: warningmark