Tag: Characterization

ScaffoldSeq – Characterization of Directed Evolution Populations

ScaffoldSeq

:: DESCRIPTION

ScaffoldSeq is software designed for the numerous applications – including directed evolution analysis – in which a user generates a population of DNA sequences encoding for partially diverse proteins with related functions and would like to characterize the single site and pairwise amino acid frequencies across the population.

::DEVELOPER

Hackel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • Python

:: DOWNLOAD

 ScaffoldSeq

:: MORE INFORMATION

Citation

ScaffoldSeq: Software for characterization of directed evolution populations.
Woldring DR, Holec PV, Hackel BJ.
Proteins. 2016 Mar 28. doi: 10.1002/prot.25040.

ClinSeK 1.2e – Targeted Variant Characterization Framework for Clinical Sequencing

ClinSeK 1.2e

:: DESCRIPTION

ClinSeK is a targeted sequence analysis toolkit that allows quick and sensitive investigation of genetic variation at sites of interest from high-throughput sequencing data.

::DEVELOPER

Zhou lab

:: SCREENSHOTS

N/A

::  REQUIREMENTS

  • Linux

:: DOWNLOAD

 ClinSeK

:: MORE INFORMATION

Citation

ClinSeK: a targeted variant characterization framework for clinical sequencing.
Zhou W, Zhao H, Chong Z, Mark RJ, Eterovic AK, Meric-Bernstam F, Chen K.
Genome Med. 2015 Mar 31;7(1):34. doi: 10.1186/s13073-015-0155-1.

FIRE-pro 1.1 – Motif Discovery and Characterization program in Proteins based on Mutual Information

FIRE-pro 1.1

:: DESCRIPTION

FIRE-pro (Finding Informative Regulatory Elements in proteins) is a motif discovery and characterization program for proteins based on mutual information

::DEVELOPER

Tavazoie lab at Columbia University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Perl

:: DOWNLOAD

 FIRE-pro

:: MORE INFORMATION

Citation:

PLoS One. 2010 Dec 29;5(12):e14444. doi: 10.1371/journal.pone.0014444.
Large-scale discovery and characterization of protein regulatory motifs in eukaryotes.
Lieber DS, Elemento O, Tavazoie S.

FIRE 1.1a – Motif Discovery and Characterization program based on Mutual Information

FIRE 1.1a

:: DESCRIPTION

FIRE (Finding Informative Regulatory Elements) is a motif discovery and characterization program based on mutual information

::DEVELOPER

Tavazoie lab at Columbia University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Perl

:: DOWNLOAD

 FIRE

:: MORE INFORMATION

Citation:

Mol Cell. 2007 Oct 26;28(2):337-50.
A universal framework for regulatory element discovery across all genomes and data types.
Elemento O, Slonim N, Tavazoie S.

ICQ-lincRNA – Identification, Characterization, and Quantification of Long Intergenic Non-Coding RNAs

ICQ-lincRNA

:: DESCRIPTION

ICQ-lincRNA offers an end-to-end solution to identify and annotate expressed lincRNAs in next generation RNA sequencing data

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / VirtualBox

:: DOWNLOAD

 ICQ-lincRNA

:: MORE INFORMATION

Citation

Hu G, Gupta SK, Troska TP, Nair A, Gupta M.
Long non-coding RNA profile in mantle cell lymphoma identifies a functional lncRNA ROR1-AS1 associated with EZH2/PRC2 complex.
Oncotarget. 2017 May 17;8(46):80223-80234. doi: 10.18632/oncotarget.17956. PMID: 29113297; PMCID: PMC5655192.

PALEOMIX 1.3.2 – Characterization of Ancient and Modern Genomes by SNP Detection and Phylogenomic and Metagenomic analysis

PALEOMIX 1.3.2

:: DESCRIPTION

The PALEOMIX pipeline is a user-friendly package designed for Unix-like systems and largely automates the analyses related to whole genome re-sequencing. It is compatible with a full range of sequence data and performs a series of user-defined analyses, including read trimming, collapsing of overlapping mate-pairs, read mapping, PCR duplicate removal, SNP calling, and metagenomic profiling.

::DEVELOPER

The Centre for Anthropobiology and Genomics of Toulouse

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PALEOMIX

:: MORE INFORMATION

Citation

Nat Protoc. 2014 May;9(5):1056-82. doi: 10.1038/nprot.2014.063. Epub 2014 Apr 10.
Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX.
Schubert M1, Ermini L1, Der Sarkissian C1, Jónsson H1, Ginolhac A1, Schaefer R2, Martin MD1, Fernández R1, Kircher M3, McCue M4, Willerslev E1, Orlando L1.

ChromHMM 1.20 – Chromatin State Discovery and Characterization

ChromHMM 1.20

:: DESCRIPTION

ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks.

::DEVELOPER

Kellis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/ Windows
  • Java

:: DOWNLOAD

 ChromHMM

:: MORE INFORMATION

Citation

Ernst J and Kellis M.
ChromHMM: automating chromatin-state discovery and characterization.
Nature Methods, 9:215-216, 2012.

3D-SURFER 2.0 – Real-time Search and Characterization of Protein Surfaces

3D-SURFER 2.0

:: DESCRIPTION

3D-SURFER is a web-based tool for real-time protein surface comparison and analysis. The server integrates a repertoire of methods to assist in high throughput screening and visualization of protein surface comparisons.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

3D-SURFER 2.0: web platform for real-time search and characterization of protein surfaces.
Xiong Y, Esquivel-Rodriguez J, Sael L, Kihara D.
Methods Mol Biol. 2014;1137:105-17. doi: 10.1007/978-1-4939-0366-5_8.

cleverSuite – Protein Characterization

cleverSuite

:: DESCRIPTION

the cleverSuite is an approach for large-scale characterization of protein groups.

::DEVELOPER

Tartaglia Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 1;30(11):1601-8. doi: 10.1093/bioinformatics/btu074. Epub 2014 Feb 3.
The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities.
Klus P, Bolognesi B, Agostini F, Marchese D, Zanzoni A, Tartaglia GG.

HPG Variant 1.0 – Characterization of Variants found by Next-Generation Sequencing

HPG Variant 1.0

:: DESCRIPTION

The HPG Variant (VARIant ANalysis Tool) suite is an ambitious project aimed to provide a complete suite of tools to work with genomic variation data, from VCF tools to variant profiling or genomic statistics.

::DEVELOPER

High Performance Genomics (HPG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  HPG Variant

:: MORE INFORMATION

Citation

VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing.
Medina I, De Maria A, Bleda M, Salavert F, Alonso R, Gonzalez CY, Dopazo J.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W54-8. doi: 10.1093/nar/gks572.