Genome annotation Tools

Genomepy is designed to provide a simple and straightforward way to download and use genomic data. This includes (1) searching available data, (2) showing the available metadata, (3) automatically downloading, preprocessing and matching data and (4) generating optional aligner indexes. All with sensible, yet controllable defaults. Currently, genomepy supports Ensembl, UCSC, NCBI and GENCODE.

A new gene finder based on a Generalized Hidden Markov Model. Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons.

A database which integrates together predictive information about proteins' function from a number of partner resources, giving an overview of the families that a protein belongs to and the domains and sites it contains. Users who have novel nucleotide or protein sequences that they wish to functionally characterise can use the software package InterProScan to run the scanning algorithms from the InterPro database in an integrated way. Sequences are submitted in FASTA format. Matches are then calculated against all of the required member database's signatures and the results are then output in a variety of formats.

KentUtils is a collection of UCSC command-line bioinformatic utilities for genome browser data processing, including tools for format conversion, genome annotation, sequence analysis, and manipulation of genomic data formats such as BED, BigWig, BigBed, and BAM files.

LTR_Finder (Long Terminal Repeat Finder) is an efficient program for finding full-length LTR retrotransposons in genome sequences.

LTRpred is an R package for de novo annotation and prediction of LTR retrotransposons in genome sequences, using structural features and sequence homology to identify and classify LTR retrotransposon families.

An accurate gene annotation mapping tool.

LiftoffTools is a toolkit for comparing gene annotations mapped between genome assemblies, enabling the detection and analysis of gene sequence variants, synteny, and gene copy number changes. It leverages Liftoff for annotation transfer and offers modules for analyzing protein-coding genes, gene synteny, and gene copy number.

Program for comparing, annotating, merging and tracking transcripts in GFF files.

Program for filtering, converting and manipulating GFF files

Python package for working with GFF and GTF files. It allows operations which would be complicated or time-consuming using a text-file-only approach.