NGDC BIT

Tool Configuration

Smith-Waterman local alignment of sequences

Data

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Input data text

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Parameters

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

Input data text

Upload a file

Parameters

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

Result Preview

Example output and submitted task results are displayed here.

#Runs 623

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######################################## # 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 #--------------------------------------- #---------------------------------------