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67 search results found

⚡ ♒ Rapid prokaryotic genome annotation

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

NCBI Prokaryotic Genome Annotation Pipeline

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Genome mapping and spliced alignment of cDNA or amino acid sequences

Dfast_core ⭐ 67

DDBJ Fast Annotation and Submission Tool

Genomes Pipeline ⭐ 63

MGnify genome analysis pipeline

FEELnc : FlExible Extraction of LncRNA

Phylocsf ⭐ 60

Phylogenetic analysis of multi-species genome sequence alignments to identify conserved protein-coding regions

Tesorter ⭐ 59

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes

Genomegtftools ⭐ 52

convert various features into a GFF-like file for use in genome browsers

Agfusion ⭐ 46

Python package to annotate and visualize gene fusions.

Prothint ⭐ 45

Protein hint generation pipeline for gene finding in eukaryotic genomes

Fluentdna ⭐ 43

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

Microbeannotator ⭐ 41

Pipeline for metabolic annotation of microbial genomes

Bitacora ⭐ 27

BITACORA: A Bioinformatics tool for gene family annotation

Metablastr ⭐ 27

Seamless Integration of BLAST Sequence Searches in R

Metasanity ⭐ 24

Pipeline for major biological analyses.

Crisprdisco ⭐ 21

CRISPR discovery pipeline

Swiftortho ⭐ 21

A high performance tool to identify orthologs and paralogs across genomes.

Cegma_v2 ⭐ 18

The final version 2 release of our software to detect core genes in eukaryotic genomes

Genome_collector ⭐ 17

🌠 Easily download genomes and build BLAST/Bowtie indexes in Python

Get_jgi_genomes ⭐ 16

A quick and easy way to download the genomes/predicted proteins of taxa available in JGI's Genome Portal.

Core Genome Alignment ⭐ 16

Scripts to analyze gene content and make a concatenated alignment of core genes from bacterial genomes.

Pantools ⭐ 15

Ampril Genomes ⭐ 15

scripts for the project of seven thaliana genomes assembly

Workflow for identifying and classifying homologous gene/protein sequences

Multiphate ⭐ 14

Throughput PhATE processing of draft or finished phage genomes

Coronavirus Knowledge Graph ⭐ 14

OBSOLETE: Prototype Neo4j Knowledge Graph for Coronavirus outbreaks (new version: https://github.com/sbl-sdsc/coronavirus-knowledge-

Proteome-Wide Association Study

Nanotext ⭐ 13

Proteins as words, genomes as documents.

Biobtree ⭐ 13

A bioinformatics tool to search, map and retrieve identifiers, keywords and attributes

Annotating principal splice isoforms

Phagehosts ⭐ 11

This is the complete code base used in Robert A. Edwards, Katelyn McNair, Karoline Faust, Jeroen Raes, and Bas E. Dutilh (2015) Computational approaches to predict bacteriophage–host relationships. FEMS Microbiology Reviews doi: 10.1093/femsre/fuv048

A tool to analyze synteny at the protein level.

Microbialgenomicsscripts ⭐ 10

A selection of short scripts for analyzing microbial genomes

Identifying ViRal and Circular content in metAgenomes

Map_viruses ⭐ 9

Align short reads against viral genomes in protein space

an easy to use implementation of the NCBI taxonomy database for daily use

Pygenprop ⭐ 9

A python library for programmatic usage of EBI InterPro Genome Properties.

Fungal Genome Mapping Pipeline

Coursera Bioinformatics ⭐ 9

My solution to Bioinformatics Specialization (Finding Hidden Messages in DNA; Genome Sequencing; Comparing Genes, Proteins, and Genomes; Molecular Evolution; Genomic Data Science and Clustering; Finding Mutations in DNA and Proteins; Bioinformatics Capstone: Big Data in Biology)

Pangenome_graphs ⭐ 9

Constructing pan genome graphs from "protein family" assignments

R package for microbial pangenomics

Multiphate2 ⭐ 8

multiPhATE with comparative genomics

WhatsGNU: a tool for identifying proteomic novelty

Perchlorate Metagenome 2018 ⭐ 8

Scripts used in the publication Tyler P. Barnum, Israel A. Figueroa, Charlotte I. Carlström, Lauren N. Lucas, Anna L. Engelbrektson, and John D. Coates. (2018) Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchlorate-reducing communities.

Genemark Ep Plus ⭐ 8

GeneMark-EP and -EP+: automatic eukaryotic gene prediction supported by spliced aligned proteins

Functional Dark Side.github.io ⭐ 7

Survival Analysis for Protein-Level TCGA Analysis

ChExMix: the ChIP-exo mixture model

MIML-DML : Multi-Instance Multi-Label Distance Metric Learning for Genome-Wide Protein Function Prediction

Decrippter ⭐ 6

Genome mining tool for novel RiPP BGCs

A python library for predicting phage lifestyle based on genome sequence

A pipeline for large-scale phylogeny-based protein function prediction using SIFTER (Statistical Inference of Function Through Evolutionary Relationships)

Phylogenomics Tools ⭐ 6

Scripts for automating tasks in phylogenetics with microbial genomes

Integrated region-based variants synchronization and Annotation for different inbreeding lines

Bioinformaticsfromcoursera ⭐ 6

Hgt Finder ⭐ 6

Program for finding horizontal gene transfer using BLAST result

Acrfinder ⭐ 6

AcrFinder, a tool for automated identification of Acr-Aca loci

Multigenomiccontext ⭐ 5

multiGenomicContext is a pipeline to see your protein in many genomic context as much as gbk you have.

Mig Phylogenomics ⭐ 5

MIG Meloidogyne species phylogenomics and and ploidy analysis

Bioinformatics_algorithms ⭐ 5

Python code covering some of the algorithms underlying the following fundamental topics in bioinformatics: assembling genomes, comparing DNA and protein sequences, finding regulatory motifs, analyzing genome rearrangements, identifying proteins, and many other topics.

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