ClustalW on Helix
Clustal W is a general purpose multiple alignment program for DNA or
proteins. The sensitivity of the commonly used progressive multiple sequence
alignment method has been greatly improved for the alignment of divergent
protein sequences. It is designed to be run interactively, or to assign
options via the command line.
Clustalw can be run in two ways on the Helix Systems:
- Multiple Alignment Workshop. A web interface
to Clustalw and other multiple seqence alignment programs.
- Command-line use on Helix
- For many or large sequences, it is probably better to use the command-line than a web interface. At the helix prompt, type 'clustalw'.
Version
Type 'clustalw' on Helix to see the current installed version.Sample session (user input in bold):
helix% clustalw ************************************************************** ******** CLUSTAL W (1.83) Multiple Sequence Alignments ******** ************************************************************** 1. Sequence Input From Disc 2. Multiple Alignments 3. Profile / Structure Alignments 4. Phylogenetic trees S. Execute a system command H. HELP X. EXIT (leave program) Your choice: 1 Sequences should all be in 1 file. 7 formats accepted: NBRF/PIR, EMBL/SwissProt, Pearson (Fasta), GDE, Clustal, GCG/MSF, RSF. Enter the name of the sequence file: seqs.inp Sequence format is Pearson Sequences assumed to be PROTEIN Sequence 1: chiins 110 aa Sequence 2: xenins 110 aa Sequence 3: humins 110 aa Sequence 4: monins 110 aa Sequence 5: dogins 110 aa Sequence 6: hamins 110 aa Sequence 7: bovins 110 aa Sequence 8: guiins 110 aa ************************************************************** ******** CLUSTAL W (1.83) Multiple Sequence Alignments ******** ************************************************************** 1. Sequence Input From Disc 2. Multiple Alignments 3. Profile / Structure Alignments 4. Phylogenetic trees S. Execute a system command H. HELP X. EXIT (leave program) Your choice: 2 ****** MULTIPLE ALIGNMENT MENU ****** 1. Do complete multiple alignment now (Slow/Accurate) 2. Produce guide tree file only 3. Do alignment using old guide tree file 4. Toggle Slow/Fast pairwise alignments = SLOW 5. Pairwise alignment parameters 6. Multiple alignment parameters 7. Reset gaps before alignment? = OFF 8. Toggle screen display = ON 9. Output format options S. Execute a system command H. HELP or press [RETURN] to go back to main menu Your choice: 1 Enter a name for the CLUSTAL output file [seqs.aln]: myseqs.aln Enter name for new GUIDE TREE file [seqs.dnd]: Start of Pairwise alignments Aligning... Sequences (1:2) Aligned. Score: 66 Sequences (1:3) Aligned. Score: 63 [...] Sequences (7:8) Aligned. Score: 61 Guide tree file created: [seqs.dnd] Start of Multiple Alignment There are 7 groups Aligning... Group 1: Sequences: 2 Score:2138 Group 2: Sequences: 2 Score:2373 Group 3: Sequences: 4 Score:2157 Group 4: Sequences: 5 Score:2146 Group 5: Sequences: 6 Score:1971 Group 6: Sequences: 2 Score:1972 Group 7: Sequences: 8 Score:1739 Alignment Score 13222 Consensus length = 110 CLUSTAL-Alignment file created [seqs.aln] CLUSTAL W (1.83) multiple sequence alignment dogins MALWMRLLPLLALLALWAPAPTRAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREVED bovins MALWTRLRPLLALLALWPPPPARAFVNQHLCGSHLVEALYLVCGERGFFYTPKARREVEG humins BALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAED monins BALWMRLLPLLALLALWGPDPVPAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAED hamins MTLWMRLLPLLTLLVLWEPNPAQAFVNQHLCGSHLVEALYLVCGERGFFYTPKSRRGVED guiins MALWMHLLTVLALLALWGPNTGQAFVSRHLCGSNLVETLYSVCQDDGFFYIPKDRRELED chiins BALWIRSLPLLALLVFSGPGTSYAAANQHLCGSHLVEALYLVCGERGFFYSPKARRDVEQ xenins BALWMQCLPLVLVLFFSTPNTE-ALVNQHLCGSHLVEALYLVCGDRGFFYYPKVKRDMEQ :** : .:: :* : * . * ..:*****:***:** ** : **** ** :* * dogins LQVRDVELAGAPGEGGLQPLALEGALQKRGIVEQCCTSICSLYQLENYCN bovins PQVGALELAGGPGAGG-----LEGPPQKRGIVEQCCASVCSLYQLENYCN humins LQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN monins PQVGQVELGGGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN hamins PQVAQLELGGGPGADDLQTLALEVAQQKRGIVDQCCTSICSLYQLENYCN guiins PQVEQTELGMGLGAGGLQPLALEMALQKRGIVDQCCTGTCTRHQLQSYCN chiins PLVSS---PLRGEAGVLPFQQEEYEKVKRGIVEQCCHNTCSLYQLENYCN xenins ALVSG---PQDNELDGMQLQPQEYQKMKRGIVEQCCHSTCSLFQLESYCN * . * *****:*** . *: .**:.*** Press [RETURN] to continue or X to stop: X ************************************************************** ******** CLUSTAL W (1.83) Multiple Sequence Alignments ******** ************************************************************** 1. Sequence Input From Disc 2. Multiple Alignments 3. Profile / Structure Alignments 4. Phylogenetic trees S. Execute a system command H. HELP X. EXIT (leave program) Your choice: x
- For many or large sequences, it is probably better to use the command-line than a web interface. At the helix prompt, type 'clustalw'.
Documentation
- Web-accessible: ClustalW Help
- Thompson, Higgins, and Gibson: CLUSTAL W. Nucleic Acids Res, 22: 4673-80. Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice.