BCM Search Launcher: Multiple Sequence Alignments

Cut and paste sequences here (Most ReadSeq formats accepted);
All sequences must be in the same format; See below for size/time limits.

Email address (when required):
Choose alignment method:
[H] [O] [P] [E] = [H]:Help/description; [O]:full Options form; [P]:search Parameters; [E]:Example search

ClustalW 1.8 (DNA/Protein) - Global progressive (BCM) [H] [O] [P] [E]
CAP Sequence Assembly (DNA) - Contig Assembly Program [H] [O] [P] [E]
MAP (DNA/Protein) - Global progressive in linear space (BCM) [H] [O] [P] [E]
PIMA 1.4 (Protein only) - Pattern-Induced (local) Multiple Alignment (BCM) [H] [O] [P] [E]
MSA 2.1 (Protein only) - Near-optimal sum-of-pairs global (WashU) [H] [O] [P] [E]
BLOCK MAKER (Protein only) - Finds conserved blocks in seq sets (FHCRC) [H] [O] [P] [E]

The following server returns search results via Email:

ClustalW 1.8 (DNA/Protein) - Global progressive (BCM) [H] [O] [P]
MEME 2.2 (DNA/Protein) - Multiple EM for Motif Elicitation (SDSC) [H] [O] [P] [E]
Match-Box 1.3 (Protein only) - Blocks alignment with reliability
Registration required after 10 uses. (FUNDP) [H] [O] [P] [E]

Size/Time limits for the multiple alignments are:
ClustalW 40,000 characters. ClustalW email 60,000 characters.
MAP, and PIMA:  20,000 characters and 60 minutes.
MSA:  8 sequences, 800 characters and 10 minutes.
BLOCK MAKER:  250 sequences.
MEME:  10,000 characters. Please do not submit data on Tuesday and Thursday mornings from 8:00 a.m. until 2:00 p.m. due to computer down-time. Please limit the Sequence Name to one line or less.
Match-Box; 50 sequences, 2000 characters each.

Special version of this page for the GNA-VSNS Biocomputing Course