Tag: Amino Acid

ENTPRISE / ENTPRISE-X – Predicting Human Disease-associated Amino Acid Mutations

ENTPRISE / ENTPRISE-X

:: DESCRIPTION

ENTPRISE is an algorithm for predicting human disease-associated amino acid mutations from sequence entropy and predicted protein structures

ENTPRISE-X is an algorithm for predicting human disease-associated frameshift & nonsense mutations.

::DEVELOPER

Center for the Study of Systems Biology

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ENTPRISE: An Algorithm for Predicting Human Disease-Associated Amino Acid Substitutions from Sequence Entropy and Predicted Protein Structures.
Zhou H, Gao M, Skolnick J.
PLoS One. 2016 Mar 16;11(3):e0150965. doi: 10.1371/journal.pone.0150965.

Zhou H, Gao M, Skolnick J.
ENTPRISE-X: Predicting disease-associated frameshift and nonsense mutations.
PLoS One. 2018 May 3;13(5):e0196849. doi: 10.1371/journal.pone.0196849. PMID: 29723276; PMCID: PMC5933770.

PseAAC / PseAAC-Builder 3.0 / PseAAC-General – Generating Pseudo Amino Acid Composition

PseAAC / PseAAC-Builder 3.0 / PseAAC-General

:: DESCRIPTION

PseAAC is an algorithm that could convert a protein sequence into a digital vector that could be processed by pattern recognition algorithms. The design of PseAAC incorporated the sequence order information to improve the conventional amino acid compositions. The application of pseudo amino acid composition is very common, including almost every branch of computational proteomics.

PseAAC-Builder (PseAAC-General) is a cross-platform stand-alone program for generating various special Chou’s pseudo-amino acid compositions.

::DEVELOPER

PseAAC team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows with Cygwin

:: DOWNLOAD

 PseAAC-Builder 

:: MORE INFORMATION

Citation:

Hong-Bin Shen and Kuo-Chen Chou.
PseAAC: a flexible web-server for generating various kinds of protein pseudo amino acid composition.
Analytical Biochemistry, 2008, 373: 386-388.

Anal Biochem. 2012 Jun 15;425(2):117-9. doi: 10.1016/j.ab.2012.03.015. Epub 2012 Mar 27.
PseAAC-Builder: a cross-platform stand-alone program for generating various special Chou’s pseudo-amino acid compositions.
Du P1, Wang X, Xu C, Gao Y.

Pufeng Du, Shuwang Gu, Yasen Jiao.
PseAAC-General: Fast building various modes of general form of Chou’s pseudo-amino acid composition for large-scale protein datasets.
International Journal of Molecular Sciences 15 (2014) pp.3495-3506

PseAAC – Generating Pseudo Amino Acid Composition

PseAAC

:: DESCRIPTION

PseAAC is a web-server, by which users can generate various kinds of PseAA composition to best fit their need.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PseAAC: a flexible web server for generating various kinds of protein pseudo amino acid composition.
Shen HB, Chou KC.
Anal Biochem. 2008 Feb 15;373(2):386-8. Epub 2007 Oct 13.

pfilt 1.5 – Sequence Filtering for Low-complexity, Coiled-coil and Biased Amino Acid Regions

pfilt 1.5

:: DESCRIPTION

pfilt program is designed to mask out (i.e. replace amino acid characters with Xs) regions of low complexity, coiled-coil regions and regions with extremely biased amino acid compositions. For compositional biased regions,only the overrepresented amino acids are masked.

:DEVELOPER

Bioinformatics Group – University College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  pfilt

:: MORE INFORMATION

Citation:

Jones, D.T. & Swindells, M.B. (2002)
Getting the most from PSI-BLAST.
Trends Biochem Sci. 2002 Mar;27(3):161-4.

rate4site 2.01 – Detect Conserved Amino-acid Site

rate4site 2.01

:: DESCRIPTION

rate4site is a program for detecting conserved amino-acid sites by computing the relative evolutionary rate for each site in a multiple sequence alignment.

::DEVELOPER

Mayrose Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

  rate4site

:: MORE INFORMATION

Citation

Mayrose, I., Graur, D., Ben-Tal, N., and Pupko, T. 2004.
Comparison of site-specific rate-inference methods: Bayesian methods are superior.
Mol Biol Evol 21: 1781-1791.

PutGaps Beta – DNA Gapped File from Amino Acid Alignment

PutGaps Beta

:: DESCRIPTION

PutGaps is a software to add gaps to a DNA alignment file based on its Amino Acid equivalent.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

PutGaps

:: MORE INFORMATION

ModelGenerator 0.851 – Amino Acid & Nucleotide Substitution Model Selection

ModelGenerator 0.851

:: DESCRIPTION

ModelGenerator is a model selection program that selects optimal amino acid and nucleotide substitution models from Fasta or Phylip alignments. ModelGenerator supports 56 nucleotide and 96 amino acid substitution models.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

ModelGenerator

:: MORE INFORMATION

Citation:

Thomas M Keane, Christopher J Creevey ,Melissa M Pentony, Thomas J Naughton and James O McInerney (2006)
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified,
BMC Evolutionary Biology, 6:29

Wregex 2.1 – Amino Acid Motif searching

Wregex 2.1

:: DESCRIPTION

Wregex (weighted regular expression).is a software tool for amino acid motif searching.

::DEVELOPER

EhuBio

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Wregex

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 1;30(9):1220-7. doi: 10.1093/bioinformatics/btu016. Epub 2014 Jan 9.
Prediction of nuclear export signals using weighted regular expressions (Wregex).
Prieto G1, Fullaondo A, Rodriguez JA.

Exit mobile version