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WAAFLE: a Workflow to Annotate Assemblies and Find LGT Events.
Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial communities, including the human microbiome. While methods exist to identify LGTs from sequenced isolate genomes, identifying LGTs from community metagenomes remains an open problem. To address this, we ...Tags: WAAFLE, Workflow, Annotate, Assemblies, Find, LGT, Events
947 days ago
SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences
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 20). The method has been approached with a tool (a...Tags: SMASH, alignment-free, tool, find, visualise, rearrangements, pairs, DNA, sequences
2319 days ago
MCAT: Motif Combining and Association Tool
This is a pipeline for finding motifs in fasta files.It can be run from the command line as follows: usage: orange_pipeline_refine.py [-h] [-w W] [--nmotifs NMOTIFS] [--iter ITER] [-c C][-s S] [-d] [-ff] [-v V]positive_seq negative_seq positional arguments:positive_seq the fasta file for the po...Tags: pipeline, find, motifs, fasta
1931 days ago
LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.
LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences. The Program first constructs all exact match pairs by a suffix-array based algorithm and extends them to long highly similar pairs. Then Smith-Waterman algorithm is used to adjust the ends of LTR ...Tags: LTR_Finder, efficient, program, find, full-length, LTR, retrotranspsons, genome, sequences
1931 days ago
dnaPipeTE: a pipeline designed to find, annotate and quantify Transposable Elements
dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not requ...Tags: dnaPipeTE, pipeline, find, annotate, quantify, Transposable, Elements, TEs
1719 days ago
Common methods to discover tandem repeats
Tandem repeats are DNA sequences that are repeated in a contiguous manner in the genome. These sequences are often used as genetic markers and are important in many areas of genetics and genomics research. Here are some methods for discovering tandem repeats in genomes: T...Tags: Tandem, repeats, DNA, sequences, find, methods
415 days ago
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