BOL: Related items

RAVEN: a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models

Jit — Wed, 24 Oct 2018 22:38:05 -0500

The RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox 2 is a software suite for Matlab that allows for semi-automated reconstruction of genome-scale models (GEMs). It makes use of published models and/or KEGG, MetaCyc databases, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology.

Address of the bookmark: https://github.com/SysBioChalmers/RAVEN

Blobsplorer

Jit — Tue, 14 Jun 2016 10:28:58 -0500

Blobsplorer is a tool for interactive visualization of assembled DNA sequence data ("contigs") derived from (often unintentionally) mixed-species pools. It allows the simultaneous display of GC content, coverage, and taxonomic annotation for collections of contigs with a view to separating out those belonging to different taxa.

Blobsplorer is unlikely to be of use on its own as it requires contig data to be supplied in a format that involves considerable preprocessing (see below for a description). The easiest way to use Blobsplorer is as part of a workflow using scripts from here.

Address of the bookmark: http://nematodes.org/martin/blobsplorer/blobsplorer.html

ShinyGO v0.61: Gene Ontology Enrichment Analysis + more

Jit — Wed, 03 Jun 2020 08:00:30 -0500

2/3/2020: Now published by Bioinformatics.

11/3/2019: V 0.61, Improve graphical visualization (thanks to reviewers). Interactive networks and much more.

5/20/2019: V.0.60, Annotation database updated to Ensembl 96. New bacterial and fungal genomes based on STRING-db! Just paste your gene list to get enriched GO terms and othe pathways for over 315 plant and animal species, based on annotation from Ensembl (Release 96), Ensembl plants (R. 43) and Ensembl Metazoa (R. 43). An additional 2031 genomes (including bacteria and fungi) are annotated based on STRING-db (v.10). In addition, it also produces KEGG pathway diagrams with your genes highlighted, hierarchical clustering trees and networks summarizing overlapping terms/pathways, protein-protein interaction networks, gene characterristics plots, and enriched promoter motifs.

Address of the bookmark: http://bioinformatics.sdstate.edu/go/

CNIDARIA: fast, reference-free phylogenomic clustering

Shruti Paniwala — Thu, 16 Jun 2016 17:55:17 -0500

Motivation: Identification of biological specimens is a major requirement for a range of applications. Reference-free methods analyse unprocessed sequencing data without relying on prior knowledge, but these do not scale to arbitrarily large genomes and arbitrarily large phylogenetic distances.

Results: We present Cnidaria, a practical tool for clustering genomic and transcriptomic data with no limitation on ge-nome size or phylogenetic distances. We successfully simultaneously clustered 169 genomic and transcriptomic datasets from 4 kingdoms, achieving 100% accuracy at supra-species level and 78% accuracy for species level.

Availability and Implementation: Cnidaria is written in C++ and Python and is available at http://www.ab.wur.nl/cnidaria.

Contact: Saulo Aflitos - sauloal@gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Address of the bookmark: https://github.com/sauloal/cnidaria/wiki

Understanding GO analysis

Neel — Wed, 08 Feb 2023 04:22:01 -0600

The confusion about gene ontology and gene ontology analysis can start right from the term itself. There are actually two different entities that are commonly referred to as gene ontology or “GO”:

the ontology itself, which is a set of terms with their precise definitions and defined relationships between them, and
the associations between gene products and GO terms, which are used to capture the existing knowledge about what each gene is known to do.

But the term gene ontology, or GO, is commonly used to refer to both, which is sometimes a source of potential confusion. In order to avoid this, here we will use the term “GO ontology” to describe the set of terms and their hierarchical structure and “GO annotations” to describe the set of associations between genes and GO terms.

There are 3 types of terms, or domains if you wish, in the gene ontology:

Biological Processes (BP)
Molecular Functions (MF)
Cellular Components (CC)

Address of the bookmark: https://advaitabio.com/faq-items/understanding-gene-ontology/

DarkHorse

Jit — Wed, 22 Jun 2016 05:37:38 -0500

DarkHorse is a bioinformatic method for rapid, automated identification and ranking of phylogenetically atypical proteins on a genome-wide basis. It works by selecting potential ortholog matches from a reference database of amino acid sequences, then using these matches to calculate a lineage probability index (LPI) score for each genome protein.

LPI scores are inversely proportional to the phylogenetic distance between database match sequences and the query genome. These scores are useful not only for large-scalede novo predictions of horizontally transferred proteins, but can also serve as an independent quality control test for potential horizontal transfer candidates identified by alternative methods, especially those based on nucleic acid signatures. Candidates having high LPI scores are unlikely to have been horizontally transferred, since they are highly conserved among closely related organisms.

One unique and powerful feature of the DarkHorse HGT Candidate database is the opportunity to explore the phylogenetic background of potential HGT donors as well as recipients. The breadth of the database allows not only query sequences, but also their database match partners to be evaluated for sequence similarity or novelty compared to taxonomically related organisms.

DarkHorse is configurable for varying degrees of phylogenetic granularity and protein sequence conservation. Users should consult the references cited below for a complete explanation of parameter selection and result interpretation. A brief tutorial page is also available on-line.

Address of the bookmark: http://darkhorse.ucsd.edu/download.html

DIY Transcriptomics

Abhi — Wed, 31 Jul 2024 01:19:26 -0500

A semester-long course covering best practices for the analysis of high-throughput sequencing data from gene expression (RNA-seq) studies, with a primary focus on empowering students to be independent in the use of lightweight and open-source software using the R programming language and the Bioconductor suite of packages. This course follows a hybrid format in which online lectures are paired with in-person labs where students participate in hands-on, live coding exercises using real ‘omic datasets. The course is focused on datasets and topics central to infectious disease research, immunology, and One-Health, but the concepts and approaches covered are applicable to any genomic study.

https://diytranscriptomics.com

Address of the bookmark: https://diytranscriptomics.com

Cheatsheet for Linux !!

Jit — Wed, 22 Jun 2016 07:55:06 -0500

Linux Commands Cheat Sheet

    File System

    ls — list items in current directory

    ls -l — list items in current directory and show in long format to see perimissions, size, an modification date

    ls -a — list all items in current directory, including hidden files

    ls -F — list all items in current directory and show directories with a slash and executables with a star

    ls dir — list all items in directory dir

    cd dir — change directory to dir

    cd .. — go up one directory

    cd / — go to the root directory

    cd ~ — go to to your home directory

    cd - — go to the last directory you were just in

    pwd — show present working directory

    mkdir dir — make directory dir

    rm file — remove file

    rm -r dir — remove directory dir recursively

    cp file1 file2 — copy file1 to file2

    cp -r dir1 dir2 — copy directory dir1 to dir2 recursively

    mv file1 file2 — move (rename) file1 to file2

    ln -s file link — create symbolic link to file

    touch file — create or update file

    cat file — output the contents of file

    less file — view file with page navigation

    head file — output the first 10 lines of file

    tail file — output the last 10 lines of file

    tail -f file — output the contents of file as it grows, starting with the last 10 lines

    vim file — edit file

    alias name 'command' — create an alias for a command
    System

    shutdown — shut down machine

    reboot — restart machine

    date — show the current date and time

    whoami — who you are logged in as

    finger user — display information about user

    man command — show the manual for command

    df — show disk usage

    du — show directory space usage

    free — show memory and swap usage

    whereis app — show possible locations of app

    which app — show which app will be run by default
    Process Management

    ps — display your currently active processes

    top — display all running processes

    kill pid — kill process id pid

    kill -9 pid — force kill process id pid
    Permissions

    ls -l — list items in current directory and show permissions

    chmod ugo file — change permissions of file to ugo - u is the user's permissions, g is the group's permissions, and o is everyone else's permissions. The values of u, g, and o can be any number between 0 and 7.

    7 — full permissions

    6 — read and write only

    5 — read and execute only

    4 — read only

    3 — write and execute only

    2 — write only

    1 — execute only

    0 — no permissions

    chmod 600 file — you can read and write - good for files

    chmod 700 file — you can read, write, and execute - good for scripts

    chmod 644 file — you can read and write, and everyone else can only read - good for web pages

    chmod 755 file — you can read, write, and execute, and everyone else can read and execute - good for programs that you want to share
    Networking

    wget file — download a file

    curl file — download a file

    scp user@host:file dir — secure copy a file from remote server to the dir directory on your machine

    scp file user@host:dir — secure copy a file from your machine to the dir directory on a remote server

    scp -r user@host:dir dir — secure copy the directory dir from remote server to the directory dir on your machine

    ssh user@host — connect to host as user

    ssh -p port user@host — connect to host on port as user

    ssh-copy-id user@host — add your key to host for user to enable a keyed or passwordless login

    ping host — ping host and output results

    whois domain — get information for domain

    dig domain — get DNS information for domain

    dig -x host — reverse lookup host

    lsof -i tcp:1337 — list all processes running on port 1337
    Searching

    grep pattern files — search for pattern in files

    grep -r pattern dir — search recursively for pattern in dir

    grep -rn pattern dir — search recursively for pattern in dir and show the line number found

    grep -r pattern dir --include='*.ext — search recursively for pattern in dir and only search in files with .ext extension

    command | grep pattern — search for pattern in the output of command

    find file — find all instances of file in real system

    locate file — find all instances of file using indexed database built from the updatedb command. Much faster than find

    sed -i 's/day/night/g' file — find all occurrences of day in a file and replace them with night - s means substitude and g means global - sed also supports regular expressions
    Compression

    tar cf file.tar files — create a tar named file.tar containing files

    tar xf file.tar — extract the files from file.tar

    tar czf file.tar.gz files — create a tar with Gzip compression

    tar xzf file.tar.gz — extract a tar using Gzip

    gzip file — compresses file and renames it to file.gz

    gzip -d file.gz — decompresses file.gz back to file
    Shortcuts

    ctrl+a — move cursor to beginning of line

    ctrl+f — move cursor to end of line

    alt+f — move cursor forward 1 word

    alt+b — move cursor backward 1 word

PeGAS: A Comprehensive Bioinformatic Solution for Pathogenic Bacterial Genomic Analysis

LEGE — Mon, 01 Sep 2025 01:18:10 -0500

This is PeGAS, a powerful bioinformatic tool designed for the seamless quality control, assembly, and annotation of Illumina paired-end reads specific to pathogenic bacteria. This tool integrates state-of-the-art open-source software to provide a streamlined and efficient workflow, ensuring accurate insights into the genomic makeup of pathogenic microbial strains.

Address of the bookmark: https://github.com/liviurotiul/PeGAS

SAM flags

Poonam Mahapatra — Wed, 29 Jun 2016 15:38:15 -0500

Decoding SAM flags

This utility makes it easy to identify what are the properties of a read based on its SAM flag value, or conversely, to find what the SAM Flag value would be for a given combination of properties.

To decode a given SAM flag value, just enter the number in the field below. The encoded properties will be listed under Summary below, to the right.

Address of the bookmark: https://broadinstitute.github.io/picard/explain-flags.html