Jit
Enthusiast computational biologist with business dream !!!
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doubletrouble: identify duplicated genes from whole-genome protein sequences and classify
By LEGE 732 days agobioconductor.org - doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal...MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
By Jit 2574 days agobioweb.supagro.inra.fr - MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing...Understanding reads mapping and flags !
By Jit 2508 days agoLinear, Chimeric, Supplementary, Primary and Secondary AlignmentsMany-to-many pairwise alignments of two sequence sets
By Poonam Mahapatra 2818 days agoemboss.sourceforge.net - needleall reads a set of input sequences and compares them all to one or more sequences, writing their optimal global sequence alignments to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (including gaps) of two...BLAST options, setting and defaults
By Jit 2644 days agowww.arabidopsis.org - BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul et al. (1990) and significantly improved by Altschul et al. (1997). It is a very fast search algorithm that is used to separately search protein or DNA...Termal: a fast and interactive terminal-based viewer for multiple sequence alignments
By LEGE 165 days agogithub.com - termal, a fast, interactive, terminal-based viewer for multiple sequence alignments (MSAs), designed for use on remote systems such as high-performance computing (HPC)...bedtools
By Jit 3298 days agobedtools.readthedocs.io - Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For...
Structure of Binary files used for storing sequencing data-bam and sff
Last updated 4591 days ago by Rahul AgarwalMany times bioinformatician needs to parse binary files like bam and sff. Advantage of binary files is that they occupy less space in memory with maximum information content. Link for those who looking for structure of Bam and sff...genoPlotR - plot gene and genome maps project!
By Abhimanyu Singh 2642 days agogenoplotr.r-forge.r-project.org - genoPlotR is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows the user to read from usual format such as protein table files and blast results, as well as home-made tabular files. Features Linear...gggenes: a ggplot2 extension for drawing gene arrow maps.
By BioStar 2104 days agohttp://wilkox.org/gggenes - Install the stable version of gggenes from CRAN: install.packages("gggenes") If you want the development version, install it from GitHub: devtools::install_github("wilkox/gggenes") More at https://github.com/wilkox/gggenes
