|
water |
Function
Smith-Waterman local alignmentDescription
water uses the Smith-Waterman algorithm (modified for speed enhancments) to calculate the local alignment.A local alignment searches for regions of local similarity between two sequences and need not include the entire length of the sequences. Local alignment methods are very useful for scanning databases or other circumsatnces when you wish to find matches between small regions of sequences, for example between protein domains.
Algorithm
The Smith-Waterman algorithm is a member of the class of algorithms that can calculate the best score and local alignment in the order of mn steps, (where 'n' and 'm' are the lengths of the two sequences). These dynamic programming algorithms were first developed for protein sequence comparison by Smith and Waterman, though similar methods were independently devised during the late 1960's and early 1970's for use in the fields of speech processing and computer science.Dynamic programming methods ensure the optimal local alignment by exploring all possible alignments and choosing the best. It does this by reading in a scoring matrix that contains values for every possible residue or nucleotide match. water finds an alignment with the maximum possible score where the score of an alignment is equal to the sum of the matches taken from the scoring matrix.
An important problem is the treatment of gaps, i.e., spaces inserted to optimise the alignment score. A penalty is subtracted from the score for each gap opened (the 'gap open' penalty) and a penalty is subtracted from the score for the total number of gap spaces multiplied by a cost (the 'gap extension' penalty).
Typically, the cost of extending a gap is set to be 5-10 times lower than the cost for opening a gap.
There are two ways to compute a penalty for a gap of n positions :
gap opening penalty + (n - 1) * gap extension penalty gap penalty + n * gap length penalty
The first way is used by EMBOSS and WU-BLAST
The second way is used by NCBI-BLAST, GCG, Staden and CLUSTAL.
Fasta used it for a long time the first way, but Prof. Pearson decided
recently to shift to the second.
The two methods are basically equivalent.
The Smith-Waterman algorithm contains no negative scores in the path matrix it creates. The algorithm starts the alignment at the highest path matrix score and works backwards until a cell contains zero.
See the Reference Smith et al. for details.
Usage
Here is a sample session with water
% water tsw:hba_human tsw:hbb_human Smith-Waterman local alignment. Gap opening penalty [10.0]: Gap extension penalty [0.5]: Output alignment [hba_human.water]: |
Go to the input files for this example
Go to the output files for this example
Command line arguments
Standard (Mandatory) qualifiers:
[-asequence] sequence Sequence USA
[-bsequence] seqall Sequence database USA
-gapopen float The gap open penalty is the score taken away
when a gap is created. The best value
depends on the choice of comparison matrix.
The default value assumes you are using the
EBLOSUM62 matrix for protein sequences, and
the EDNAFULL matrix for nucleotide
sequences.
-gapextend float The gap extension penalty is added to the
standard gap penalty for each base or
residue in the gap. This is how long gaps
are penalized. Usually you will expect a few
long gaps rather than many short gaps, so
the gap extension penalty should be lower
than the gap penalty. An exception is where
one or both sequences are single reads with
possible sequencing errors in which case you
would expect many single base gaps. You can
get this result by setting the gap open
penalty to zero (or very low) and using the
gap extension penalty to control gap
scoring.
[-outfile] align Output alignment file name
Additional (Optional) qualifiers:
-datafile matrixf This is the scoring matrix file used when
comparing sequences. By default it is the
file 'EBLOSUM62' (for proteins) or the file
'EDNAFULL' (for nucleic sequences). These
files are found in the 'data' directory of
the EMBOSS installation.
Advanced (Unprompted) qualifiers:
-[no]brief boolean Brief identity and similarity
Associated qualifiers:
"-asequence" associated qualifiers
-sbegin1 integer Start of the sequence to be used
-send1 integer End of the sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-sformat1 string Input sequence format
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-bsequence" associated qualifiers
-sbegin2 integer Start of each sequence to be used
-send2 integer End of each sequence to be used
-sreverse2 boolean Reverse (if DNA)
-sask2 boolean Ask for begin/end/reverse
-snucleotide2 boolean Sequence is nucleotide
-sprotein2 boolean Sequence is protein
-slower2 boolean Make lower case
-supper2 boolean Make upper case
-sformat2 string Input sequence format
-sdbname2 string Database name
-sid2 string Entryname
-ufo2 string UFO features
-fformat2 string Features format
-fopenfile2 string Features file name
"-outfile" associated qualifiers
-aformat3 string Alignment format
-aextension3 string File name extension
-adirectory3 string Output directory
-aname3 string Base file name
-awidth3 integer Alignment width
-aaccshow3 boolean Show accession number in the header
-adesshow3 boolean Show description in the header
-ausashow3 boolean Show the full USA in the alignment
-aglobal3 boolean Show the full sequence in alignment
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report deaths
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-asequence] (Parameter 1) |
Sequence USA | Readable sequence | Required |
| [-bsequence] (Parameter 2) |
Sequence database USA | Readable sequence(s) | Required |
| -gapopen | The gap open penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. | Number from 0.000 to 100.000 | 10.0 for any sequence |
| -gapextend | The gap extension penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. | Number from 0.000 to 10.000 | 0.5 for any sequence |
| [-outfile] (Parameter 3) |
Output alignment file name | Alignment output file | |
| Additional (Optional) qualifiers | Allowed values | Default | |
| -datafile | This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAFULL for DNA |
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -[no]brief | Brief identity and similarity | Boolean value Yes/No | Yes |
Input file format
water reads any two sequence USAs of the same type (DNA or protein).Input files for usage example
'tsw:hba_human' is a sequence entry in the example protein database 'tsw'
Database entry: tsw:hba_human
ID HBA_HUMAN STANDARD; PRT; 141 AA.
AC P01922;
DT 21-JUL-1986 (Rel. 01, Created)
DT 21-JUL-1986 (Rel. 01, Last sequence update)
DT 15-JUL-1999 (Rel. 38, Last annotation update)
DE HEMOGLOBIN ALPHA CHAIN.
GN HBA1 AND HBA2.
OS Homo sapiens (Human), Pan troglodytes (Chimpanzee), and
OS Pan paniscus (Pygmy chimpanzee) (Bonobo).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN [1]
RP SEQUENCE FROM N.A. (ALPHA-1).
RX MEDLINE; 81088339.
RA MICHELSON A.M., ORKIN S.H.;
RT "The 3' untranslated regions of the duplicated human alpha-globin
RT genes are unexpectedly divergent.";
RL Cell 22:371-377(1980).
RN [2]
RP SEQUENCE FROM N.A. (ALPHA-2).
RX MEDLINE; 81175088.
RA LIEBHABER S.A., GOOSSENS M.J., KAN Y.W.;
RT "Cloning and complete nucleotide sequence of human 5'-alpha-globin
RT gene.";
RL Proc. Natl. Acad. Sci. U.S.A. 77:7054-7058(1980).
RN [3]
RP SEQUENCE FROM N.A. (ALPHA-2).
RX MEDLINE; 80137531.
RA WILSON J.T., WILSON L.B., REDDY V.B., CAVALLESCO C., GHOSH P.K.,
RA DERIEL J.K., FORGET B.G., WEISSMAN S.M.;
RT "Nucleotide sequence of the coding portion of human alpha globin
RT messenger RNA.";
RL J. Biol. Chem. 255:2807-2815(1980).
RN [4]
RP SEQUENCE FROM N.A. (ALPHA-1 AND ALPHA-2).
RA FLINT J., HIGGS D.R.;
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP SEQUENCE.
RA BRAUNITZER G., GEHRING-MULLER R., HILSCHMANN N., HILSE K., HOBOM G.,
RA RUDLOFF V., WITTMANN-LIEBOLD B.;
RT "The constitution of normal adult human haemoglobin.";
RL Hoppe-Seyler's Z. Physiol. Chem. 325:283-286(1961).
RN [6]
RP SEQUENCE.
RA HILL R.J., KONIGSBERG W.;
RT "The structure of human hemoglobin: IV. The chymotryptic digestion of
RT the alpha chain of human hemoglobin.";
RL J. Biol. Chem. 237:3151-3156(1962).
RN [7]
[Part of this file has been deleted for brevity]
FT /FTId=VAR_002841.
FT VARIANT 130 130 A -> D (IN YUDA; O2 AFFINITY DOWN).
FT /FTId=VAR_002842.
FT VARIANT 131 131 S -> P (IN QUESTEMBERT; HIGHLY UNSTABLE;
FT CAUSES ALPHA-THALASSEMIA).
FT /FTId=VAR_002843.
FT VARIANT 133 133 S -> R (IN VAL DE MARNE; O2 AFFINITY UP).
FT /FTId=VAR_002844.
FT VARIANT 135 135 V -> E (IN PAVIE).
FT /FTId=VAR_002845.
FT VARIANT 136 136 L -> M (IN CHICAGO).
FT /FTId=VAR_002846.
FT VARIANT 136 136 L -> P (IN BIBBA; UNSTABLE;
FT CAUSES ALPHA-THALASSEMIA).
FT /FTId=VAR_002847.
FT VARIANT 138 138 S -> P (IN ATTLEBORO; O2 AFFINITY UP).
FT /FTId=VAR_002848.
FT VARIANT 139 139 K -> E (IN HANAKAMI; O2 AFFINITY UP).
FT /FTId=VAR_002849.
FT VARIANT 139 139 K -> T (IN TOKONAME; O2 AFFINITY UP).
FT /FTId=VAR_002850.
FT VARIANT 140 140 Y -> H (IN ROUEN; O2 AFFINITY UP).
FT /FTId=VAR_002851.
FT VARIANT 141 141 R -> C (IN NUNOBIKI; O2 AFFINITY UP).
FT /FTId=VAR_002852.
FT VARIANT 141 141 R -> L (IN LEGNANO; O2 AFFINITY UP).
FT /FTId=VAR_002853.
FT VARIANT 141 141 R -> H (IN SURESNES; O2 AFFINITY UP).
FT /FTId=VAR_002854.
FT VARIANT 141 141 R -> P (IN SINGAPORE).
FT /FTId=VAR_002855.
FT HELIX 4 35
FT HELIX 37 42
FT TURN 44 45
FT TURN 50 51
FT HELIX 53 71
FT TURN 72 74
FT HELIX 76 79
FT TURN 80 80
FT HELIX 81 89
FT TURN 90 91
FT TURN 95 95
FT HELIX 96 112
FT TURN 114 116
FT HELIX 119 136
FT TURN 137 139
SQ SEQUENCE 141 AA; 15126 MW; 5EC7DB1E CRC32;
VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK
KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA
VHASLDKFLA SVSTVLTSKY R
//
|
Database entry: tsw:hbb_human
ID HBB_HUMAN STANDARD; PRT; 146 AA.
AC P02023;
DT 21-JUL-1986 (Rel. 01, Created)
DT 21-JUL-1986 (Rel. 01, Last sequence update)
DT 15-JUL-1999 (Rel. 38, Last annotation update)
DE HEMOGLOBIN BETA CHAIN.
GN HBB.
OS Homo sapiens (Human), Pan troglodytes (Chimpanzee), and
OS Pan paniscus (Pygmy chimpanzee) (Bonobo).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN [1]
RP SEQUENCE.
RC SPECIES=HUMAN;
RA BRAUNITZER G., GEHRING-MULLER R., HILSCHMANN N., HILSE K., HOBOM G.,
RA RUDLOFF V., WITTMANN-LIEBOLD B.;
RT "The constitution of normal adult human haemoglobin.";
RL Hoppe-Seyler's Z. Physiol. Chem. 325:283-286(1961).
RN [2]
RP SEQUENCE FROM N.A.
RC SPECIES=HUMAN;
RX MEDLINE; 81064667.
RA LAWN R.M., EFSTRATIADIS A., O'CONNELL C., MANIATIS T.;
RT "The nucleotide sequence of the human beta-globin gene.";
RL Cell 21:647-651(1980).
RN [3]
RP SEQUENCE OF 121-146 FROM N.A.
RC SPECIES=HUMAN;
RX MEDLINE; 85205333.
RA LANG K.M., SPRITZ R.A.;
RT "Cloning specific complete polyadenylylated 3'-terminal cDNA
RT segments.";
RL Gene 33:191-196(1985).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF DEOXYHEMOGLOBIN.
RC SPECIES=HUMAN;
RX MEDLINE; 76027820.
RA FERMI G.;
RT "Three-dimensional fourier synthesis of human deoxyhaemoglobin at
RT 2.5-A resolution: refinement of the atomic model.";
RL J. Mol. Biol. 97:237-256(1975).
RN [5]
RP SEQUENCE.
RC SPECIES=P.TROGLODYTES;
RX MEDLINE; 66071496.
RA RIFKIN D.B., KONIGSBERG W.;
RT "The characterization of the tryptic peptides from the hemoglobin of
RT the chimpanzee (Pan troglodytes).";
RL Biochim. Biophys. Acta 104:457-461(1965).
RN [6]
[Part of this file has been deleted for brevity]
FT VARIANT 140 140 A -> T (IN ST JACQUES: O2 AFFINITY UP).
FT /FTId=VAR_003081.
FT VARIANT 140 140 A -> V (IN PUTTELANGE; POLYCYTHEMIA;
FT O2 AFFINITY UP).
FT /FTId=VAR_003082.
FT VARIANT 141 141 L -> R (IN OLMSTED; UNSTABLE).
FT /FTId=VAR_003083.
FT VARIANT 142 142 A -> D (IN OHIO; O2 AFFINITY UP).
FT /FTId=VAR_003084.
FT VARIANT 143 143 H -> D (IN RANCHO MIRAGE).
FT /FTId=VAR_003085.
FT VARIANT 143 143 H -> Q (IN LITTLE ROCK; O2 AFFINITY UP).
FT /FTId=VAR_003086.
FT VARIANT 143 143 H -> P (IN SYRACUSE; O2 AFFINITY UP).
FT /FTId=VAR_003087.
FT VARIANT 143 143 H -> R (IN ABRUZZO; O2 AFFINITY UP).
FT /FTId=VAR_003088.
FT VARIANT 144 144 K -> E (IN MITO; O2 AFFINITY UP).
FT /FTId=VAR_003089.
FT VARIANT 145 145 Y -> C (IN RAINIER; O2 AFFINITY UP).
FT /FTId=VAR_003090.
FT VARIANT 145 145 Y -> H (IN BETHESDA; O2 AFFINITY UP).
FT /FTId=VAR_003091.
FT VARIANT 146 146 H -> D (IN HIROSHIMA; O2 AFFINITY UP).
FT /FTId=VAR_003092.
FT VARIANT 146 146 H -> L (IN COWTOWN; O2 AFFINITY UP).
FT /FTId=VAR_003093.
FT VARIANT 146 146 H -> P (IN YORK; O2 AFFINITY UP).
FT /FTId=VAR_003094.
FT VARIANT 146 146 H -> Q (IN KODAIRA; O2 AFFINITY UP).
FT /FTId=VAR_003095.
FT HELIX 5 15
FT TURN 16 17
FT HELIX 20 34
FT HELIX 36 41
FT HELIX 43 45
FT HELIX 51 55
FT TURN 56 56
FT HELIX 58 75
FT TURN 76 77
FT HELIX 78 94
FT TURN 95 96
FT TURN 100 100
FT HELIX 101 121
FT HELIX 124 142
FT TURN 143 144
SQ SEQUENCE 146 AA; 15867 MW; EC9744C9 CRC32;
VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK
EFTPPVQAAY QKVVAGVANA LAHKYH
//
|
Output file format
The output is a standard EMBOSS alignment file.
The results can be output in one of several styles by using the command-line qualifier -aformat xxx, where 'xxx' is replaced by the name of the required format. Some of the alignment formats can cope with an unlimited number of sequences, while others are only for pairs of sequences.
The available multiple alignment format names are: unknown, multiple, simple, fasta, msf, trace, srs
The available pairwise alignment format names are: pair, markx0, markx1, markx2, markx3, markx10, srspair, score
See: http://emboss.sf.net/docs/themes/AlignFormats.html for further information on alignment formats.
Output files for usage example
File: hba_human.water
########################################
# Program: water
# Rundate: Fri Jul 15 2005 12:00:00
# Align_format: srspair
# Report_file: hba_human.water
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: HBA_HUMAN
# 2: HBB_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 145
# Identity: 63/145 (43.4%)
# Similarity: 88/145 (60.7%)
# Gaps: 8/145 ( 5.5%)
# Score: 293.5
#
#
#=======================================
HBA_HUMAN 2 LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLS- 49
|:|.:|:.|.|.|||| :..|.|.|||.|:.:.:|.|:.:|..| |||
HBB_HUMAN 3 LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLST 50
HBA_HUMAN 50 ----HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDP 95
.|:.:||.|||||..|.::.:||:|::....:.||:||..||.|||
HBB_HUMAN 51 PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDP 100
HBA_HUMAN 96 VNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKY 140
.||:||.:.|:..||.|...||||.|.|:..|.:|.|:..|..||
HBB_HUMAN 101 ENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKY 145
#---------------------------------------
#---------------------------------------
|
The Identity: is the percentage of identical matches between the two sequences over the reported aligned region (including any gaps in the length).
The Similarity: is the percentage of matches between the two sequences over the reported aligned region (including any gaps in the length).
Data files
For protein sequences EBLOSUM62 is used for the substitution matrix. For nucleotide sequence, EDNAFULL is used. Others can be specified.
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata
Notes
water is a true implementation of the Smith-Waterman algorithm and so produces a full path matrix. It therefore cannot be used with genome sized sequences unless you have a lot of memory and a lot of time.References
- Smith TF, Waterman MS (1981) J. Mol. Biol 147(1);195-7
Warnings
Local alignment methods only report the best matching areas between two sequences - there may be a large number of alternative local alignments that do not score as highly. If two proteins share more than one common region, for example one has a single copy of a particular domain while the other has two copies, it may be possible to "miss" the second and subsequent alignments. You will be able to see this situation if you have done a dotplot and your local alignment does not show all the features you expected to see.water is for aligning the best matching subsequences of two sequences. It does not necessarily align whole sequences against each other; you should use needle if you wish to align closely related sequences along their whole lengths.
A true Smith Waterman implementation like water needs memory proportional to the product of the sequence lengths. For two sequences of length 10,000,000 and 1,000 it therefore needs memory proportional to 10,000,000,000 characters. Two arrays of this size are produced, one of ints and one of floats so multiply that figure by 8 to get the memory usage in bytes. That doesn't include other overheads. Therefore only use water and needle for accurate alignment of reasonably short sequences.
If you run out of memory, try using supermatcher or matcher.
Diagnostic Error Messages
Uncaught exception Assertion failed raised at ajmem.c:xxx
Probably means you have run out of memory. Try using supermatcher or matcher if this happens.
Exit status
0 if successful.Known bugs
None.See also
| Program name | Description |
|---|---|
| matcher | Finds the best local alignments between two sequences |
| seqmatchall | All-against-all comparison of a set of sequences |
| supermatcher | Match large sequences against one or more other sequences |
| wordmatch | Finds all exact matches of a given size between 2 sequences |
matcher is a local alignment program that gives as good an alignment as
water
but it uses far less memory. However,water
runs twice as fast as matcher.supermatcher is designed for local alignments of very large sequences. It gives good results as long as there is not significant amounts of insertion or deletion in the alignment.
supermatcher Finds a match of a large sequence against one or more sequences matcher Finds the best local alignments between two sequences
Author(s)
Alan Bleasby (ajb © ebi.ac.uk)European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
History
Completed 7th July 1999.Modified 27th July 1999 - tweaking scoring.
Modified 22 Oct 2000 - added ID and Similarity scores.