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We are still working on this page. Tools will be added and opened gradually until the end of August, the date of the first complete version of this web site. You can find more about the schedule in "what's next ?"
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Sequence alignment
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Choose the appropriate set of aligned sequence

Write the reference protein used for the numbering of residues (bovin chymotrypsin by default).


Write or paste the Swiss-Prot descriptive codes or accession numbers of the selected sequences and separated them by a space.


Select the window for alignment editing from residue to (heavy chain of chymotrypsin by default)

Select the type of display:
horizontal, vertical
black&white
aa properties color-coded
identity (red %) and similarity (blue % for matrix and corresponding threshold ) color-coded


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View a window in the sequence alignment (looking for motif ?)
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Choose the appropriate set of aligned sequence

Select the window for alignment editing from residue to in the absolute numbering of the multialigned domain. Smaller window, faster transfert and easier reading.


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release

Submit your sequence to v1.7 (Thompson, J.D. et al, 1994) at PIR

Insert sequences with their ID lines in FASTA format (e.g. >Unique ID)

or PIR entry codes.

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Multiple Sequence Alignment at WU with Ctree, Clustal or MSA from your file of sequences

File of sequences to align

*

Program Alignment confidence cutoff (only used in ctree)

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release

Submit your sequence to BCM Search Launcher at the Baylor College of Medicine

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 1.3 (Protein only) - Blocks alignment with reliability
Registration required after 10 uses. (FUNDP) [H] [O] [P] [E]
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[HomePage] [Sequence Index] [Sequence Analyser] [Mutations] [Evolution] [Tour-Tutorial] [Help]
[Structure Index] [Structure Analyzer] [Ligands] [Function][About] [Contact_us][Setup][Search] [Links]

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Go to the School of MedicineGo to the Department of Biochemistry and Molecular Biophysics


Thierry Rose, PhD and Enrico Di Cera, MD
Department of Biochemistry and Molecular Biophysics
Washington University School of Medicine
Saint Louis, MO, U.S.A.

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