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Tools for Searching Repeats And Palindromic Sequences
Last updated 3094 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...Predict Gene Ontology with sequences !
By LEGE 2280 days agoekhidna2.biocenter.helsinki.fi - 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...SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences
By Jit 3209 days agogithub.com - SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences. The detection is based on relative compression, namely using a FCM, also known as Markov model, of high context order (typically...S-plot2: creates an interactive, two-dimensional heatmap of sequences
By Jit 2929 days agobitbucket.org - S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryotic chromosomes and smaller prokaryotic genomes can...SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences
By Jit 2853 days agolbbe.univ-lyon1.fr - 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...Kalign: fast multiple sequence alignment program for biological sequences.
By BioStar 2530 days agogithub.com - Kalign is a fast multiple sequence alignment program for biological sequences. Align sequences and output the alignment in MSF format: kalign -i BB11001.tfa -f msf -o out.msf Align sequences and output the alignment in clustal format: kalign...IgBLAST 1.17 is now available with improved identification of productive V gene sequences
By Jit 2163 days agoIgBLAST 1.17 is now available with improved identification of productive V gene sequencesSteps to find palindrome in genomes !
By BioStar 1306 days agoPalindromes are sequences of nucleotides that read the same backward as forward.Jaeger : an accurate and fast deep-learning tool to detect bacteriophage sequences
By Neel 417 days agogithub.com - Jaeger is a tool that utilizes homology-free machine learning to identify phage genome sequences that are hidden within metagenomes. It is capable of detecting both phages and prophages within metagenomic assemblies. The performance of the Jaeger...Scallop: reference-based transcriptome assembler for RNA-seq
By Rahul Nayak 3072 days agogithub.com - Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improvement through a novel algorithm that can be...
