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Home Sequence alignment
Needle
Sequences type
Protein
Nucleotide
Protein

Data

Sequence A
Example file
Sequence(s) B
Example file

Parameters

false
True
False
EDNAFULL
DNAFULL
DNAMAT
pair
Pair
Markx0
Markx1
Markx2
Markx3
Markx10
Srspair
Score
Clustal
Fasta
Msf
Nexus
Phylip
Selex
References 
Needleman, S. B. and Wunsch, C. D. (1970) J. Mol. Biol. 48, 443-453.
Kruskal, J. B. (1983) An overview of squence comparison In D. Sankoff and J. B. Kruskal, (ed.), Time warps, string edits and macromolecules: the theory and practice of sequence comparison, pp. 1-44 Addison Wesley.
Instructions 

Needleman-Wunsch global alignment of two sequences

needle reads two input sequences and writes their optimal global sequence alignment to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two sequences along their entire length. The algorithm uses a dynamic programming method to ensure the alignment is optimum, by exploring all possible alignments and choosing the best. A scoring matrix is read that contains values for every possible residue or nucleotide match. Needle finds the 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, minus penalties arising from opening and extending gaps in the aligned sequences. The substitution matrix and gap opening and extension penalties are user-specified.

Contributor(s)
Yingke Ma
bit@big.ac.cn

Data

Sequence A
Example file
Sequence(s) B
Example file

Parameters

false
True
False
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 
Needleman, S. B. and Wunsch, C. D. (1970) J. Mol. Biol. 48, 443-453.
Kruskal, J. B. (1983) An overview of squence comparison In D. Sankoff and J. B. Kruskal, (ed.), Time warps, string edits and macromolecules: the theory and practice of sequence comparison, pp. 1-44 Addison Wesley.
Instructions 

Needleman-Wunsch global alignment of two sequences

needle reads two input sequences and writes their optimal global sequence alignment to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two sequences along their entire length. The algorithm uses a dynamic programming method to ensure the alignment is optimum, by exploring all possible alignments and choosing the best. A scoring matrix is read that contains values for every possible residue or nucleotide match. Needle finds the 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, minus penalties arising from opening and extending gaps in the aligned sequences. The substitution matrix and gap opening and extension penalties are user-specified.

Contributor(s)
Yingke Ma
bit@big.ac.cn
Open Result 
########################################
# Program: needle
# Rundate: Sun 20 Mar 2022 20:11:57
# Commandline: needle
#    -asequence asequence.faa
#    -bsequence bsequence.faa
#    -outfile output_protein.needle
# Align_format: srspair
# Report_file: output_protein.needle
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: hba_human
# 2: hbb_human
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 149
# Identity:      65/149 (43.6%)
# Similarity:    90/149 (60.4%)
# Gaps:           9/149 ( 6.0%)
# Score: 292.5
# 
#
#=======================================

hba_human          1 MV-LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-D     48
                     || |:|.:|:.|.|.||||  :..|.|.|||.|:.:.:|.|:.:|..| |
hbb_human          1 MVHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGD     48

hba_human         49 LS-----HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLR     93
                     ||     .|:.:||.|||||..|.::.:||:|::....:.||:||..||.
hbb_human         49 LSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLH     98

hba_human         94 VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR    142
                     |||.||:||.:.|:..||.|...||||.|.|:..|.:|.|:..|..||.
hbb_human         99 VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH    147


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