EMBOSS: emma

Program emma

Function

Multiple alignment program - interface to ClustalW program

Description

EMMA calculates the multiple alignment of nucleic acid or protein sequences according to the method of Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994).

This is an interface to the ClustalW distribution.

Usage

Here is an example session with emma.


% 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]

Command line arguments

   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

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

Input file format

The input is two or more sequences.

Output file format

emma writes the aligned sequences and a dendrogram file showing how the sequences were clusterd during the progressive alignments.

The clustalw output sequeces are reformatted into EMBOSS output.

Data files

The comparison matrices available for clustalw in carrying out a protein sequence alignment are:

blosum
pam
gonnet
id
user defined

The comparison matrices available for clustalw in carrying out a nucleotide sequence alignment are:

iub
clustalw
user defined

Notes

This is an interface to the ClustalW application

References

Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice." Nucleic Acids Research, 22:4673-4680.

Warnings

Diagnostic Error Messages

Exit status

Known bugs

Author(s)

This application was written by Mark Faller (mfaller@hgmp.mrc.ac.uk)

History

Completed 18 February 1999

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.