BOL: Related items

Bioinformatics Codes Search

Jitendra Narayan — Thu, 15 Aug 2013 11:08:52 -0500

I bet, this website will be your best friend in near future. This helps us to explore the existing open source codes and learn from it.

You can find some useful open source bioinformatics codes for your analysis work. You can use the left bar options to filtere out or narrow down your search result. This webpage can be an useful resource for a beginners bioinformatician as it contain several bioinformatics basics script that are commonly used by biological programmers and biologist.

Stand on the slumped, dandruff-covered shoulders of millions of computer nerds. _/\_

Enjoy the code and research work.

http://code.ohloh.net/search?s=bioinformatics

Address of the bookmark: http://code.ohloh.net/search?s=bioinformatics

Stand-alone programs for Bioinformatician

Radha Agarkar — Sat, 21 May 2016 22:50:15 -0500

This directory contains applications for stand-alone use, built specifically for a Linux 64-bit machine.

For help on the bigBed and bigWig applications see:
http://genome.ucsc.edu/goldenPath/help/bigBed.html
http://genome.ucsc.edu/goldenPath/help/bigWig.html

View the file 'FOOTER' to see the usage statement for each of the applications.

Address of the bookmark: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

VCFtools: perform common tasks with VCF files such as file validation, file merging, intersecting, complements

Rahul Nayak — Tue, 07 Aug 2018 10:01:46 -0500

VCFtools contains a Perl API (Vcf.pm) and a number of Perl scripts that can be used to perform common tasks with VCF files such as file validation, file merging, intersecting, complements, etc. The Perl tools support all versions of the VCF specification (3.2, 3.3, 4.0, 4.1 and 4.2), nevertheless, the users are encouraged to use the latest versions VCFv4.1 or VCFv4.2. The VCFtools in general have been used mainly with diploid data, but the Perl tools aim to support polyploid data as well. Run any of the Perl scripts with the --help switch to obtain more help.

Many of the Perl scripts require that the VCF files are compressed by bgzip and indexed by tabix (both tools are part of the tabix package, available for download here). The VCF files can be compressed and indexed using the following commands

bgzip my_file.vcf
tabix -p vcf my_file.vcf.gz

http://vcftools.sourceforge.net/perl_module.html

Address of the bookmark: http://vcftools.sourceforge.net/perl_module.html

LAST

Archana Malhotra — Wed, 09 Mar 2016 14:27:01 -0600

LAST can:

Handle big sequence data, e.g:
- Compare two vertebrate genomes
- Align billions of DNA reads to a genome
Indicate the reliability of each aligned column.
Use sequence quality data properly.
Compare DNA to proteins, with frameshifts.
Compare PSSMs to sequences
Calculate the likelihood of chance similarities between random sequences.
Do split and spliced alignment.
Train alignment parameters for unusual kinds of sequence (e.g. nanopore).

Address of the bookmark: http://last.cbrc.jp/

Predict Gene Ontology with sequences !

LEGE — Wed, 08 Jul 2020 04:59:28 -0500

PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function. The tool is designed to predict the functional description (DE) and GO classes.

PANNZER2 processes bacterial proteomes in minutes and eukaryotic proteomes in an hour. You can use AAI-profiler to summarize a proteome's species neighbors and reveal taxonomic identity or contamination.

http://ekhidna2.biocenter.helsinki.fi/sanspanz/

IterPro is for the beginners

h ttps://www.ebi.ac.uk/interpro/

You can find other comparative info at https://academic.oup.com/view-large/118391389

Address of the bookmark: http://ekhidna2.biocenter.helsinki.fi/sanspanz/

ACANA: An accurate and consistent alignment tool for DNA sequences

Jit — Wed, 06 Dec 2017 09:45:29 -0600

ACANA is an accurate and consistent alignment tool for DNA sequences. ACANA is specifically designed for aligning sequences that share only some moderately conserved regions and/or have a high frequency of long insertions or deletions. It attempts to combine the best of local and global alignments algorithms in searching for evolutionarily related regions of sequences in order to achieve the best alignment. ACANA is also robust to the small changes of alignment parameters, particularly the gap extension score. As an accurate alignment tool, ACANA is particularly useful in comparative sequence analysis for identifying conserved functional regulatory elements.

Address of the bookmark: https://www.niehs.nih.gov/research/resources/software/biostatistics/acana/index.cfm

GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome sequences

Jit — Fri, 28 Sep 2018 09:35:10 -0500

GRSR is a Tool for Deriving Genome Rearrangement Scenarios for Multiple Uni-chromosomal Genomes. This tool will do the following steps:

Step 1. Run mugsy to get multiple sequence alignment results.
Step 2 & 3. Extraction of the Coordinates of Core Blocks, Construction of Synteny Blocks and Generating Signed Permutations.
Step 4. Generate pairwise genome rearrangement scenarios and find repeats at the breakpoints of each rearrangement events.

https://github.com/DanwangJessica/GRSR

Address of the bookmark: https://github.com/DanwangJessica/GRSR

SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences

Jit — Wed, 12 Dec 2018 09:22:41 -0600

The software package SiLiX implements an ultra-efficient algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints.

SiLiX adopts a graph-theoretical framework to interpret similarity pairs as edges of a network. A very efficient algorithm, based on the Disjoint Sets Data Structure, allows the computation of sequence families with low time and space requirements.

A parallel version of SiLiX, based on MPI, is also available in this package and has been proved to be scalable, so that its allows the study of very large datasets.

SiLiX is already included in the analysis pipeline for HOGENOM.

Address of the bookmark: http://lbbe.univ-lyon1.fr/SiLiX?lang=fr

Miropeats: discovers regions of sequence similarity amongst any set of DNA sequences

Poonam Mahapatra — Mon, 26 Aug 2019 17:55:24 -0500

Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and then presents this similarity information graphically. Sequence similarity searching is a very general tool that forms the basis of many different biological sequence analyses but it is limited by the verbosity of traditional alignment presentation styles. Miropeats enhances the utility of conventional DNA sequence comparisons when looking at long lengths of sequence similarity by summarizing extensive large scale sequence similarities on a single page of graphics. The latest version of Miropeats can be used as a general pairwise alignment program or in its traditional role sorting out a big mess of overlapping or similar regions.

Address of the bookmark: http://www.littlest.co.uk/software/bioinf/old_packages/miropeats/

NucDiff: In-depth characterization and annotation of differences between two sets of DNA sequences

Jit — Tue, 05 May 2020 10:35:48 -0500

NucDiff locates and categorizes differences between two closely related nucleotide sequences. It is able to deal with very fragmented genomes, structural rearrangements and various local differences. These features make NucDiff to be perfectly suitable to compare assemblies with each other or with available reference genomes.

NucDiff provides information about the types of differences and their locations. It is possible to upload the results into genome browser for visualization and further inspection. It was written in Python and uses the NUCmer package from MUMmer[1] for sequence comparison.

Address of the bookmark: https://github.com/uio-cels/NucDiff