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Protocols

SWAKK specifications

Information


Unique identifier OMICS_22479
Name SWAKK
Alternative name Sliding Window Analysis of Ka and Ks
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data A pair of coding DNA sequences and a reference protein structure.
Input format PDB+FASTA
Output data A 2D graph and, if available, a 3D structure.
Programming languages Perl
Computer skills Basic
Version 2.1
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline Han Liang
  • person_outline Laura Landweber

Additional information


http://ibl.mdanderson.org/swakk/faq.html

Publication for Sliding Window Analysis of Ka and Ks

SWAKK citations

 (11)
library_books

One prophage WO gene rescues cytoplasmic incompatibility in Drosophila melanogaster

2018
Proc Natl Acad Sci U S A
PMCID: 5948995
PMID: 29686091
DOI: 10.1073/pnas.1800650115

[…] of neutrality demonstrate that closely related (76.2–99.8% pairwise nucleotide identity) type I cifA homologs () largely evolve by purifying selection (Fig. S4 A and B), and sliding window analyses [sliding window analysis of Ka and Ks (SWAKK) and Java codon delimited alignment, JCoDA] reveal that purifying selection is strongest on the catalase-rel domain and the unannotated region at the N term […]

call_split

HIV Progression Depends on Codon and Amino Acid Usage Profile of Envelope Protein and Associated Host Genetic Influence

2017
Front Microbiol
PMCID: 5471322
PMID: 28663742
DOI: 10.3389/fmicb.2017.01083
call_split See protocol

[…] jobori, ; Yang, ) (http://abacus.gene.ucl.ac.uk/software/paml.html) with runmode = −2 and CodonFreq = 1.Evolutionary rate of each individual residue for a given env gene sequence was calculated using SWAKK server (http://ibl.mdanderson.org/swakk/) (Liang et al., ). It estimates the ratio of non-synonymous to synonymous substitution rates (Ka/Ks) between a pair of protein-coding DNA sequences, by a […]

library_books

Molecular evolution of WDR62, a gene that regulates neocorticogenesis

2016
PMCID: 4833054
PMID: 27114917
DOI: 10.1016/j.mgene.2016.02.005

[…] hologous coding sequence of WDR62. Ka − Ks was calculated at the sliding increment of 10 codons (30 nucleotides) and the results are obtained in the graph drawn by the GNUPLOT software implemented in SWAKK (). The non-synonymous substitutions within positively selected segments (Ka/Ks > 1) are categorized according to their physicochemical properties by using BLOSSUM 62 ().Domains were allocated t […]

library_books

Nucleolin Regulates Phosphorylation and Nuclear Export of Fibroblast Growth Factor 1 (FGF1)

2014
PLoS One
PMCID: 3942467
PMID: 24595027
DOI: 10.1371/journal.pone.0090687

[…] Potential interaction sites on the surface of the FGF1 molecule were determined using the bioinformatic web servers meta-PPISP , ConSurf and SWAKK . 18 surface mutations disturbing putative binding sites were selected and introduced using the Quick Change Site-Directed Mutagenesis protocol (Stratagene). […]

call_split

Evidence for Conserved Function of γ–Glutamyltranspeptidase in Helicobacter Genus

2012
PLoS One
PMCID: 3279353
PMID: 22348013
DOI: 10.1371/journal.pone.0030543
call_split See protocol

[…] selected by FindModel (http://www.hiv.lanl.gov/). Trees were visualized by iTOL . Non-synonymous/synonymous substitution (Ka∶Ks) was evaluated by sliding window analysis (window size of 50 bp) using SWAKK . […]

library_books

Computational and Biochemical Analysis of the Xanthomonas Effector AvrBs2 and Its Role in the Modulation of Xanthomonas Type Three Effector Delivery

2011
PLoS Pathog
PMCID: 3228805
PMID: 22144898
DOI: 10.1371/journal.ppat.1002408

[…] ulence in a range of different host plant species. In addition, PAML analysis revealed a significant variation in the ω ratio over the length of the avrBs2 sequence. Sliding window analysis using the SWAKK program was used to determine the distribution of variation in the ω ratio across avrBs2 from Xe and Xcc. The low ω over the GDE-virulence region is consistent with purifying selection to maint […]

Citations

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SWAKK institution(s)
Department of Chemistry, Princeton Plasma Physics Laboratory, Princeton University, Princeton, NJ, USA; Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
SWAKK funding source(s)
Supported by National Institute of General Medical Sciences grant GM59708.

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