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Tools for Searching Repeats And Palindromic Sequences
Last updated 2414 days ago by Poonam Mahapatra Comments (2)What are genomic interspersed repeats? In the mid 1960's scientists discovered that many genomes contain stretches of highly repetitive DNA sequences ( see Reassociation Kinetics Experiments, and C-Value Paradox ). These sequences were later...CSBB-v1.0
By Neel 3069 days agogithub.com - CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R and python in background for specific modules....Finding Patterns in Biological Sequences
By Jit 2893 days agoengr.case.edu - In this report we provide an overview of known techniques for discovery of patterns of biological sequences (DNA and proteins). We also provide biological motivation, and methods of biological verification of such patterns. Finally we list publicly...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 2810 days agoStructural variation caller tools using long reads-
Bioinformatics tools to detect horizontal gene transfer (HGT) in genomes
Last updated 1052 days ago by AbhiHorizontal gene transfer (HGT), the “non-sexual movement of genetic material between two organisms” , is relatively common in prokaryotes and single-celled eukaryotes, but a number of factors combine to make it far rarer in... -
Protein-Protein Interaction Sites Predictions !
Last updated 2404 days ago by Poonam MahapatraThe study of Protein–Protein Interactions (PPIs) has a crucial role in biology, medicine and the pharmaceutical industry. PPIs can be investigated from two aspects: The interaction partners of a specific protein and the amino acid residues... MITObim - mitochondrial baiting and iterative mapping
By Rahul Nayak 2392 days agogithub.com - This document contains instructions on how to use the MITObim pipeline described in Hahn et al. 2013. The full article can be found here. Kindly cite the article if you are using MITObim in your work. The pipeline was originally developed...MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
By Rahul Nayak 2388 days agogithub.com - MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and...gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
By Rahul Nayak 1765 days agogithub.com - gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and...Tools for Differential expression analysis
By Abhi 747 days ago Comments (1)the sequenced reads can be mapped to the organism’s genes to assess how differently the genes are expressed under the experimental circumstances as opposed to the control scenario. This is known as differential expression (DE) analysis
