SNAP 20080926 / FlexSnap 20091128 – Non-sequential Pair-wise Structural Alignment

SNAP 20080926 / FlexSnap 20091128

:: DESCRIPTION

SNAP finds non-sequential 3D protein structure alignments. It was initially called STSA

FlexSnap allows the ability to find both flexible and non-sequential allignments.

::DEVELOPER

Mohammed J. Zaki

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 SNAP , FlexSnap

:: MORE INFORMATION

Citation

Saeed Salem, Mohammed J. Zaki and Chris Bystroff,
Iterative Non-Sequential Protein Structural Alignment.
Journal of Bioinformatics and Computational Biology, 7(3):571-596. Jun 2009

Algorithms Mol Biol. 2010 Jan 4;5:12. doi: 10.1186/1748-7188-5-12.
FlexSnap: flexible non-sequential protein structure alignment.
Salem S1, Zaki MJ, Bystroff C.

SNAP 1.0b18 – Scalable Nucleotide Alignment Program

SNAP 1.0b18

:: DESCRIPTION

SNAP is a fast and accurate aligner for short DNA reads. It is optimized for modern read lengths of 100 bases or higher, and takes advantage of these reads to align data quickly through a hash-based indexing scheme.

::DEVELOPER

the UC Berkeley AMP Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 SNAP

:: MORE INFORMATION

Citation

Matei Zaharia, William J. Bolosky, Kristal Curtis, Armando Fox, David Patterson, Scott Shenker, Ion Stoica, Richard M. Karp, and Taylor Sittler.
Faster and More Accurate Sequence Alignment with SNAP.
arXiv:1111.5572v1, November 2011.

SNAP 20131129 – Gene Prediction tool.

SNAP 20131129

:: DESCRIPTION

SNAP (Semi-HMM-based Nucleic Acid Parser) is a gene prediction tool.

::DEVELOPER

Korf Lab at the University of California, Davis.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 SNAP

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2004 May 14;5:59.
Gene finding in novel genomes.
Korf I.

SNAP 1.1.1 – Synonymous/Non-synonymous Analysis Program

SNAP 1.1.1

:: DESCRIPTION

SNAP calculates synonymous and non-synonymous substitution rates based on a set of codon-aligned nucleotide sequences. It outputs a synonymous and a non-synonymous distance matrix, an exhaustive pairwise codon-by-codon comparison, and a summary table.

::DEVELOPER

Bette Korber at Los Alamos National Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • perl

:: DOWNLOAD

  SNAP

:: MORE INFORMATION

Citation

Korber B. (2000)
HIV Signature and Sequence Variation Analysis.
Computational Analysis of HIV Molecular Sequences, Chapter 4, pages 55-72.
Allen G. Rodrigo and Gerald H. Learn, eds. Dordrecht, Netherlands: Kluwer Academic Publishers.

SNaP – Simulation of sNp haplotype data And Phenotypic traits

SNaP

:: DESCRIPTION

The SNaP program can be used to generate SNP haplotype sequence data of unrelated individuals and nuclear families with a fixed or random number of children.

::DEVELOPER

Statistical Genetics and Bioinformatics Group, Cologne Center for Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows
:: DOWNLOAD

  SNaP

:: MORE INFORMATION

Citation

Nothnagel M (2002).
Simulation of LD block-structured SNP haplotype data and its use for the analysis of case-control data by supervised learning methods.
Am J Hum Genet 71 (Suppl.)(4): A2363.

SNAP 2.2 – Identification and Annotation of proxy SNPs using HapMap

SNAP 2.2

:: DESCRIPTION

SNAP is a web server for finding and annotating proxy SNPs based on linkage disequilibrium, genomic location, and coverage by commercial genotyping arrays.

::DEVELOPER

Broad Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Johnson, A. D., Handsaker, R. E., Pulit, S., Nizzari, M. M., O’Donnell, C. J., de Bakker, P. I. W.
SNAP: A web-based tool for identification and annotation of proxy SNPs using HapMap
Bioinformatics, 2008 24(24):2938-2939

SNAP – Predicts Effect of Mutations on Protein Function

SNAP

:: DESCRIPTION

SNAP (screening for non-acceptable polymorphisms) is a method for evaluating effects of single amino acid substitutions on protein function.SNAP identifies over 80% of the non-neutral mutations at 77% accuracy and over 76% of the neutral mutations at 80% accuracy at its default threshold. Each prediction is associated with a reliability index that correlates with accuracy and thereby enables experimentalists to zoom into the most promising predictions.

::DEVELOPER

Yana Bromberg in Rost Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 available upon request.

:: MORE INFORMATION

Citation

SNAP predicts effect of mutations on protein function.
Bromberg Y, Yachdav G, Rost B.
Bioinformatics. 2008 Oct 15;24(20):2397-8. Epub 2008 Aug 30.

SNAP Workbench 2.0 – Analysis programs for making Inferences on Population processes

SNAP Workbench 2.0

:: DESCRIPTION

SNAP (Suite of Nucleotide Analysis Programs) Workbench is a Java program that manages and coordinates a series of analysis programs for making inferences on population processes. SNAP workbench allows the user to customize the implementation of complex console programs and functions for the purpose of automating and enhancing data exploration. In our implementation, the workbench facilitates population parameter estimation by ensuring that the assumptions and program limitations of each analysis method are met and by providing a step-by-step methodology to effectively integrate both summary-statistic methods and coalescent-based population genetic models.

SNAP Map is a command line-based tool that collapses DNA sequence data into unique haplotypes, extracts variable sites, and manipulates output into multiple formats for input into existing software packages for evolutionary analyses.  Map includes novel features such as recoding indels, including or excluding variable sites that violate an infinite-sites model and the option of collapsing sequences with corresponding phenotypic information, important in testing for significant haplotype-phenotype associations.

SNAP Combine is a command-line based tool that merges the contents of multiple single locus DNA sequence files into a single multi-locus output file. There are various input and output file formats. The files can be merged into a union or intersection of all the input loci. Additionally Combine tracks the start and end positions of each file allowing the user to exclude variable sites or taxa, important in creating input files for multilocus analyses.

::DEVELOPER

the Carbone lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Java
:: DOWNLOAD

  SNAP Workbench

:: MORE INFORMATION

Citation

Aylor, D. L., Price, E.W. and I. Carbone. 2006.
SNAP: Combine and Map modules for multilocus population genetic analysis.
Bioinformatics 22:1399-1401.