VTDB_HUMAN VTDB_HUMAN (*) Clustalw cuts off Fasta labels after the first space (e.g. ">abc def" becomes ">abc").
Sequence alignment Consensus key (see documentation for details) * - single, fully conserved residue : - conservation of strong groups . - conservation of weak groups - no consensus CLUSTAL W (1.81) multiple sequence alignment FETA_HUMAN
Clustal W options and diagnostic messages Alignment type: Protein
Alignment order: aligned
Pairwise alignment parameters Method: accurate Matrix: Gonnet Gap open penalty: 10.00
Gap extension penalty: 0.10
Multiple alignment parameters Matrix: Gonnet Gap open penalty: 10.00 % identity for delay: 30 Penalize end gaps: on Gap separation distance: 0
Negative matrix?: no Gap extension penalty: 0.20 Residue-specific gap penalties: on Hydrophilic gap penalties: on Hydrophilic residues: GPSNDQEKR
CLUSTAL W (1.81) Multiple Sequence Alignments
Sequence type explicitly set to Protein Sequence format is Pearson Sequence 1: VTDB_HUMAN 474 aa Sequence 2: FETA_HUMAN 609 aa Sequence 3: ALBU_HUMAN 609 aa Sequence 4: AFAM_HUMAN 599 aa Start of Pairwise alignments Aligning... Sequences (1:2) Aligned. Score: 16 Sequences (1:3) Aligned. Score: 21 Sequences (1:4) Aligned. Score: 19 Sequences (2:3) Aligned. Score: 40 Sequences (2:4) Aligned. Score: 39 Sequences (3:4) Aligned. Score: 34 Time for pairwise alignment: 0.220557 http://seqtool.sdsc.edu/CGI/BW.cgi#!
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Biology WorkBench 3.2 - CLUSTALW
10/14/03 10:21 AM
Guide tree file created: [../tmp-dir/5018.CLUSTALW.dnd] Start of Multiple Alignment There are 3 groups Aligning... Group 1: Sequences: 2 Score:9194 Group 2: Sequences: 3 Score:9103 Group 3: Delayed Sequence:1 Score:4072 Time for multiple alignment: 0.350931 Alignment Score 5845 CLUSTAL-Alignment file created
[../tmp-dir/5018.CLUSTALW.aln]
Import Alignment(s) Return Help Report Bugs
Citation Algorithm Citation: Higgins, D.G., Bleasby, A.J. and Fuchs, R. (1992) CLUSTAL V: improved software for multiple sequence alignment. Computer Applications in the Biosciences (CABIOS), 8(2):189-191. Thompson J.D., Higgins D.G., Gibson T.J. "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice." Nucleic Acids Res. 22:4673-4680(1994). Felsenstein, J. 1989. PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166. Program Citation: CLUSTAL W: Julie D. Thompson, Desmond G. Higgins and Toby J. Gibson, modified; any errors are due to the modifications. PHYLIP: Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle. Copyright (C) 1999, Board of Trustees of the University of Illinois.
