Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Stephen F. Altschul, John C. Wootton, E. Michael Gertz, Richa
Agarwala, Aleksandr Morgulis, Alejandro A. Schäffer, and Yi-Kuo Yu
(2005) "Protein database searches using compositionally adjusted
substitution matrices", FEBS J. 272:5101-5109.
Reports are generated on using all sequences producing significant
alignments. To generate reports on a subset of sequences, use the
report links in the Descriptions tab while selecting specific sequences.
Subject sequences can be removed or added from within the Descriptions tab and the selections will carry through to the other tabbed views.
Use the formats in Download to save data for selected sequences. Manage Columns adds and subtracts data columns from the Descriptions table.
Use the click outs to see the selected results in
GenPept
, Graphical Sequence Viewer, BLAST Tree View, COBALT multiple sequence alignment.
The graphic is an overview of the database sequences aligned
to the query sequence. These are represented horizontal bars colored
coded by score and showing the extent
of the alignment on the query sequence. Separate aligned
regions on the same database sequence are connected by a thin grey line.
Mousing over an alignment shows the database sequence title.
Clicking an alignment displays a box with more details about the
alignment and
link to the sequence alignment itself in the Alignments
section of the report.
Alignment view: Choose how to view alignments.
The default "pairwise" view shows how each subject sequence aligns
individually to the query sequence. The "query-anchored" view shows how
all subject sequences align to the query sequence. For each view type,
you can choose to show "identities" (matching residues) as letters or dots.
more...
CDS feature: Show annotated coding region and translation.
more...
Line length: Number of letters to show on one line in an alignment.