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Data

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Input data text:

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Parameters

Matrix

Gap open

Gap extend

Result format

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

Input data text:

Upload a file

Example file

Input data text:

Upload a file

Example file

Parameters

Matrix

Gap open

Gap extend

Result format

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


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