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 1.7 (DNA/Protein) - Global progressive (BCM) [H] [O] [P] [E]
 CAP Sequence Assembly (DNA) - Contig Assembly Program (TIGEM) [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 1.7 (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 (Protein) - 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.

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 Special version of this page for the GNA-VSNS Biocomputing Course
 Back to BCM Search Launcher Home Page

Page Curator: Kim C. Worley, Human Genome Center, Baylor College of Medicine  (sl-help@dot.bcm.tmc.edu).
Last modified: Tue Oct 13 15:57:50 CDT 1998
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