CleanCollapse 1.0.5 – Transfer Alignment of Sequences into Single Sequence

CleanCollapse 1.0.5

:: DESCRIPTION

CleanCollapse is a relatively user-friendly Windows program that accepts an alignment of sequences, and optionally can remove rare sporadic polymorphisms that may represent analytical artifacts, and also reduce redundancy by “collapsing” identical sequences into a single sequence. The program provides a record of these manipulation, and some rudimentary analysis (e.g. proportion of synonymous and nonsynonymous sporadic changes) that may assist interpretation

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

CleanCollapse

:: MORE INFORMATION

Before you download software you need to read disclaimer.

 

PDBtool v4.80 – Extract Structural Features from original PDB File

PDBtool v4.80

:: DESCRIPTION

PDBtool is an integrated software for handling PDB file. This tool could parse the coordinate, do SEQRES-ATOM mapping, calculate secondary structure and solvent accessibility, compute conformational letter, and reconstruct missing residues.

::DEVELOPER

Sheng Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

PDBtool

:: MORE INFORMATION

SISEQ 1.59.4 – A Simple Sequence Manipulation tool

SISEQ 1.59.4

:: DESCRIPTION

SISEQ has been developed to extract sequence informations from large database entries and to manipulate sequence informations for input to various sequence analysis software.

::DEVELOPER

Sato Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • TCL/TK

:: DOWNLOAD

  SISEQ

:: MORE INFORMATION

Citation

Bioinformatics. 2000 Feb;16(2):180-1.
SISEQ: manipulation of multiple sequence and large database files for common platforms.
Sato N.

MMCIF Dictionary Suite 2.300 – Parse, Validate, Manage data dictionaries used by the PDB

MMCIF Dictionary Suite 2.300

:: DESCRIPTION

MMCIF Dictionary Suite is a collection of tools to parse, validate, manage data dictionaries used by the PDB. Applications are also included, which convert data dictionaries to XML schema, provide HTML browsing, produce mapping information for relational database loaders (Db Loader) and convert data files between related CIF dialects

::DEVELOPER

RCSB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

   MMCIF Dictionary Suite

:: MORE INFORMATION

PreMeta – Exchange of Information between four software packages for Meta-analysis

PreMeta

:: DESCRIPTION

PreMeta is a software program written in C++ that is designed to facilitate the exchange of information between four software packages for meta-analysis of rare-variant associations: MASS, RAREMETAL, MetaSKAT, and seqMeta.

::DEVELOPER

Danyu Lin

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

PreMeta

:: MORE INFORMATION

Citation

Tang ZZ, Bunn P, Tao R, Liu Z, Lin DY.
PreMeta: a tool to facilitate meta-analysis of rare-variant associations.
BMC Genomics. 2017 Feb 14;18(1):160. doi: 10.1186/s12864-017-3573-1. PMID: 28196472; PMCID: PMC5310051.

BioPAX2SBML – Translation of BioPAX into SBML including the Qualitative Models extension

BioPAX2SBML

:: DESCRIPTION

BioPAX2SBML is a  webtool. It is capable of properly translating BioPAX formats (Level 2 and 3) into SBML format (Level 3 Version 1 with qual) including reactions and relations in one model.

::DEVELOPER

the Interfaculty Institute for Biomedical Informatics (IBMI)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

  BioPAX2SBML

:: MORE INFORMATION

Citation

Büchel F, Wrzodek C, Mittag F, Dräger A, Eichner J, Rodriguez N, Le Novère N, and Zell A.
Qualitative translation of relations from BioPAX to SBML.
Bioinformatics (2012) 28 (20): 2648-2653.

SBML2LATEX 0.9.9 – Conversion of SBML files into Human-readable Reports

SBML2LATEX 0.9.9

:: DESCRIPTION

SBML2LATEX is a tool to convert files in the System Biology Markup Language SBML) format into LATEX files.

::DEVELOPER

the Interfaculty Institute for Biomedical Informatics (IBMI)

:: SCREENSHOTS

SBML2LATEX

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Java

:: DOWNLOAD

  SBML2LATEX

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Jun 1;25(11):1455-6. doi: 10.1093/bioinformatics/btp170. Epub 2009 Mar 23.
SBML2L(A)T(E)X: conversion of SBML files into human-readable reports.
Dräger A, Planatscher H, Motsou Wouamba D, Schröder A, Hucka M, Endler L, Golebiewski M, Müller W, Zell A.