PDBQT Converter 20110806 – Convert .mol2 and .pdb Files to .pdbqt Format

PDBQT Converter 20110806

:: DESCRIPTION

PDBQT converter can help you convert a batch of .pdb or .mol2 or a mix of these files to .pdbqt files.

::DEVELOPER

Dr M Murali Krishna Kumar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • .net framework

:: DOWNLOAD

 PDBQT Converter

:: MORE INFORMATION

STR_ConvertFormats 20120306 – Transform STR typing data to Genotyper table format

STR_ConvertFormats 20120306

:: DESCRIPTION

STR_ConvertFormats is an Excel-based tool developed to transform STR typing data from tables where every row contains information from a single locus (e.g., GeneMapperID output format) to a format where every row contains all typing results for a single sample (e.g., Genotyper table format).

::DEVELOPER

Dave Duewer at National Institute of Standards and Technolog

:: SCREENSHOTS

:: REQUIREMENTS

  • Excel

:: DOWNLOAD

STR_ConvertFormats

:: MORE INFORMATION

Citation

See description in Becky Hill presentation at the Expert Systems Workshop held in conjunction with the 2nd Annual Present and Future Technological Advances in Human Identification Conference (Roanoke, VA), March 27, 2006, “NIST Experience with FSS-i3 software

Repbase Submitter 1.1.115 – Format & Annotate Repbase Entries

Repbase Submitter 1.1.115

:: DESCRIPTION

RepbaseSubmitteris a java-based interface for formatting and annotating Repbase entries. It eliminates many common formatting errors, and automates actions such as calculation of sequence lengths and composition, thus facilitating curation of Repbase sequences. In addition, it has several features for predicting protein coding regions in sequences; searching and including Pubmed references in Repbase entries; and searching the NCBI taxonomy database for correct inclusion of species information and taxonomic position.

:: DEVELOPER

Genetic Information Research Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  Repbase Submitter

:: MORE INFORMATION

Citation:

Kohany O, Gentles AJ, Hankus L, Jurka J
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.
BMC Bioinformatics, 2006 Oct 25;7:474

Haplotyper 1.0 – Genotype Format Data from an Excel File to a Format of Arlequin

Haplotyper 1.0

:: DESCRIPTION

Haplotyper (Genotype Transposer) is an excel macro that will format data from an Excel spreadsheet to a format ready to be used by the program “Arlequin“, which will reconstruct haplotype frequencies within the population, based on the genotypes given.  After which, other macros will extract the haplotype information, calculate linkage disequilibrium between markers, and prepare an input sheet for the “GOLD” program, which makes a graphical display of this data.  Then, a last macro can reconstruct the haplotypes of each individual in the population, using a maximum likelihood method and the haplotypes present in the population as proposed by Arlequin.

::DEVELOPER

David G. Cox

:: SCREENSHOTS

:: REQUIREMENTS

  • EXCEL

:: DOWNLOAD

Haplotyper

:: MORE INFORMATION

haplotyper has evolved into PHARE

 

PDBCNS 2.0 – Interconvert Atom Names between PDB & CNS formats

PDBCNS 2.0

:: DESCRIPTION

PDBCNS is a perl script to convert atom names for common amino acids and nucleic acid bases from PDB format to CNS (or XPLOR) style atom names.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

:: DOWNLOAD

PDBCNS

:: MORE INFORMATION

PDBCNS is free software available under the terms of its own BSD-style license.