Serine protease: Sequence Analyzer

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Family ID	AC ID	Number trltor	Seq.Viewer	Score
Select	Keywords	Close to	Motif	Filter	Set operators
Save/read set	Align	Align custom	Window	AA freq	Specific

Sequence alignment

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

View a window in the sequence alignment (looking for motif ?)

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

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

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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Go 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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