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EMBOSS: emma |
This is an interface to the ClustalW distribution.
% emma Input sequence: globins.fasta Output sequence [hbahum.aln]: Output file [hbahum.dnd]: ..clustalw17 -infile=5345A -outfile=5345B -align -type=protein ... CLUSTAL W (1.74) Multiple Sequence Alignments Sequence type explicitly set to Protein Sequence format is Pearson Sequence 1: hbahum 141 aa Sequence 2: hbbhum 146 aa Sequence 3: hbghum 146 aa Sequence 4: hbhagf 148 aa Sequence 5: hbrlam 149 aa Sequence 6: mycrhi 151 aa Sequence 7: myohum 153 aa Start of Pairwise alignments Aligning... Sequences (1:2) Aligned. Score: 41 Sequences (1:3) Aligned. Score: 39 Sequences (1:4) Aligned. Score: 21 Sequences (1:5) Aligned. Score: 27 Sequences (1:6) Aligned. Score: 13 Sequences (1:7) Aligned. Score: 26 Sequences (2:3) Aligned. Score: 73 Sequences (2:4) Aligned. Score: 19 Sequences (2:5) Aligned. Score: 19 Sequences (2:6) Aligned. Score: 15 Sequences (2:7) Aligned. Score: 24 Sequences (3:4) Aligned. Score: 21 Sequences (3:5) Aligned. Score: 21 Sequences (3:6) Aligned. Score: 15 Sequences (3:7) Aligned. Score: 23 Sequences (4:5) Aligned. Score: 41 Sequences (4:6) Aligned. Score: 12 Sequences (4:7) Aligned. Score: 16 Sequences (5:6) Aligned. Score: 17 Sequences (5:7) Aligned. Score: 18 Sequences (6:7) Aligned. Score: 11 Guide tree file created: [5345C] Start of Multiple Alignment There are 6 groups Aligning... Group 1: Sequences: 2 Score:883 Group 2: Sequences: 2 Score:2344 Group 3: Sequences: 3 Score:934 Group 4: Delayed Group 5: Sequences: 5 Score:950 Group 6: Delayed Sequence:7 Score:1046 Sequence:6 Score:986 Alignment Score 1746 GCG-Alignment file created [5345B]
Mandatory qualifiers (* if not always prompted): [-inseqs] seqall Sequence database USA [-outseq] seqoutset The sequence alignment output filename [-dendoutfile] outfile The dendogram output filename * -dendfile string name of old dendrogram file * -pwgapc float slow pairwise alignment: gap opening penalty * -pwgapv float slow pairwise alignment: gap extension penalty * -pwmatrix select Select matrix * -pwdnamatrix select Select matrix * -pairwisedata string Filename of user pairwise matrix * -ktup integer fast pairwise alignment: similarity scores: K-Tuple size * -gapw integer fast pairwise alignment: similarity scores: gap penalty * -topdiags integer fast pairwise alignment: similarity scores: number of diagonals to be considered * -window integer fast pairwise alignment: similarity scores: diagonal window size * -nopercent bool fast pairwise alignment: similarity scores: suppresses percentage score * -mamatrix string Filename of user multiple alignment matrix Optional qualifiers (* if not always prompted): -onlydend bool only produce dendrogram file * -dend bool select if you want to do alignment using an old dendrogram -insist bool Insist that the sequence type is changed to protein -slowfast select Please select one * -matrix select Select matrix * -dnamatrix select Select matrix -gapc float Multiple alignment: gap penalty -gapv float Multiple alignment: variable gap penalty * -unweighted bool Transitions are unweighted -[no]endgaps bool use end gap separation penalty -gapdist integer gap separation penalty range * -norgap bool no residue specific gaps * -hgapres string list of hydrophilic residues * -nohgap bool no hydrophilic gaps -maxdiv integer cut-off to delay the alignment of the most divergent sequences in a data set Advanced qualifiers: -tmpprot bool Temporary holder for input protein sequence type -prot bool Protein input sequence -slow bool Slow and accurate alignment -displayslow bool Prompt for slow alignment options -usermatrix bool User defined matrix required -umatrix bool User defined matrix (not used) -displayfast bool Prompt for fast alignment options -usermamatrix bool Prompt for user multiple alignment matrix -umamatrix bool User defined multiple alignment matrix |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-inseqs] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
[-outseq] (Parameter 2) |
The sequence alignment output filename | Writeable sequences | <sequence>.format |
[-dendoutfile] (Parameter 3) |
The dendogram output filename | Output file | <sequence>.emma |
-dendfile | name of old dendrogram file | Any string is accepted | NULL |
-pwgapc | slow pairwise alignment: gap opening penalty | Number 0.000 or more | 10.0 |
-pwgapv | slow pairwise alignment: gap extension penalty | Number 0.000 or more | 0.1 |
-pwmatrix | Select matrix | blosum pam gonnet id own |
blosum |
-pwdnamatrix | Select matrix | iub clustalw own |
iub |
-pairwisedata | Filename of user pairwise matrix | Any string is accepted | NULL |
-ktup | fast pairwise alignment: similarity scores: K-Tuple size | integer from 0 to 4 | 1 for protein, 2 for nucleic |
-gapw | fast pairwise alignment: similarity scores: gap penalty | Positive integer | 3 for protein, 5 for nucleic |
-topdiags | fast pairwise alignment: similarity scores: number of diagonals to be considered | Positive integer | 5 for protein, 4 for nucleic |
-window | fast pairwise alignment: similarity scores: diagonal window size | Positive integer | 5 for protein, 4 for nucleic |
-nopercent | fast pairwise alignment: similarity scores: suppresses percentage score | Yes/No | No |
-mamatrix | Filename of user multiple alignment matrix | Any string is accepted | NULL |
Optional qualifiers | Allowed values | Default | |
-onlydend | only produce dendrogram file | Yes/No | No |
-dend | select if you want to do alignment using an old dendrogram | Yes/No | No |
-insist | Insist that the sequence type is changed to protein | Yes/No | No |
-slowfast | Please select one | slow fast |
slow |
-matrix | Select matrix | blosum pam gonnet id own |
blosum |
-dnamatrix | Select matrix | iub clustalw own |
iub |
-gapc | Multiple alignment: gap penalty | Positive foating point number | 10.0 |
-gapv | Multiple alignment: variable gap penalty | Positive foating point number | 5.0 |
-unweighted | Transitions are unweighted | Yes/No | No |
-[no]endgaps | use end gap separation penalty | Yes/No | Yes |
-gapdist | gap separation penalty range | Positive integer | 8 |
-norgap | no residue specific gaps | Yes/No | No |
-hgapres | list of hydrophilic residues | Any string is accepted | GPSNDQEKR |
-nohgap | no hydrophilic gaps | Yes/No | No |
-maxdiv | cut-off to delay the alignment of the most divergent sequences in a data set | Integer from 0 to 100 | 30 |
Advanced qualifiers | Allowed values | Default | |
-tmpprot | Temporary holder for input protein sequence type | Yes/No | Yes for protein sequences |
-prot | Protein input sequence | Yes/No | Yes if -insist was set |
-slow | Slow and accurate alignment | Yes/No | Yes unless -slowfast is 'fast' |
-displayslow | Prompt for slow alignment options | Yes/No | Yes if -options and -slow are both set |
-usermatrix | User defined matrix required | Yes/No | Yes if -pwmatrix is set |
-umatrix | User defined matrix (not used) | Yes/No | Yes if -pwdnamatrix is set |
-displayfast | Prompt for fast alignment options | Yes/No | Yes if -options is true and -slow is false |
-usermamatrix | Prompt for user multiple alignment matrix | Yes/No | True if -matrix was set |
-umamatrix | User defined multiple alignment matrix | Yes/No | True if -dnamatrix was set |
The clustalw output sequeces are reformatted into EMBOSS output.
Program name | Description |
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Other EMBOSS intefaces to the ClustalW package functions.