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Sequence alignment
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Water
Sequences type
Protein
Nucleotide
Protein

Data

Sequence A
Example file
Sequence B
Example file

Parameters

EDNAFULL
DNAFULL
DNAMAT
pair
Pair
Markx0
Markx1
Markx2
Markx3
Markx10
Srspair
Score
Clustal
Fasta
Msf
Nexus
Phylip
Selex
References 
Smith TF, Waterman MS (1981) J. Mol. Biol 147(1);195-7
Instructions 

Smith-Waterman local alignment of sequences

water uses the Smith-Waterman algorithm (modified for speed enhancments) to calculate the local alignment of a sequence to one or more other sequences. The gap insertion penalty, gap extension penalty and substitution matrix used to calculate the alignments are specified. The output is a standard EMBOSS alignment file.

Contributor(s)
Zhenglin Du
bit@big.ac.cn

Data

Sequence A
Example file
Sequence B
Example file

Parameters

EBLOSUM62
BLOSUM30
BLOSUM35
BLOSUM40
BLOSUM45
BLOSUM50
BLOSUM55
BLOSUM60
BLOSUM62
BLOSUM75
BLOSUM80
BLOSUM85
BLOSUM90
BLOSUM Clustered
PAM10
PAM20
PAM30
PAM40
PAM50
PAM60
PAM70
PAM80
PAM90
PAM100
PAM110
PAM120
PAM130
PAM140
PAM150
PAM160
PAM170
PAM180
PAM190
PAM200
PAM210
PAM220
PAM230
PAM240
PAM250
PAM260
PAM270
PAM280
PAM290
PAM300
PAM310
PAM320
PAM330
PAM340
PAM350
PAM360
PAM370
PAM380
PAM390
PAM400
PAM410
PAM420
PAM430
PAM440
PAM450
PAM460
PAM470
PAM480
PAM490
PAM500
pair
Pair
Markx0
Markx1
Markx2
Markx3
Markx10
Srspair
Score
Clustal
Fasta
Msf
Nexus
Phylip
Selex
References 
Smith TF, Waterman MS (1981) J. Mol. Biol 147(1);195-7
Instructions 

Smith-Waterman local alignment of sequences

water uses the Smith-Waterman algorithm (modified for speed enhancments) to calculate the local alignment of a sequence to one or more other sequences. The gap insertion penalty, gap extension penalty and substitution matrix used to calculate the alignments are specified. The output is a standard EMBOSS alignment file.

Contributor(s)
Zhenglin Du
bit@big.ac.cn
Open Result
######################################## # Program: water # Rundate: Mon 21 Mar 2022 19:29:31 # Commandline: water # -asequence sequence_a.faa # -bsequence sequence_b.faa # -outfile output_protein.water # Align_format: srspair # Report_file: output_protein.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 3 LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLS- 50 |:|.:|:.|.|.|||| :..|.|.|||.|:.:.:|.|:.:|..| ||| hbb_human 4 LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLST 51 hba_human 51 ----HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDP 96 .|:.:||.|||||..|.::.:||:|::....:.||:||..||.||| hbb_human 52 PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDP 101 hba_human 97 VNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKY 141 .||:||.:.|:..||.|...||||.|.|:..|.:|.|:..|..|| hbb_human 102 ENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKY 146 #--------------------------------------- #---------------------------------------