BOL: Related items

SATSUMA : Highly sensitive whole-genome synteny alignments.

Jit — Fri, 13 May 2016 05:25:26 -0500

Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes, non-coding genes, or neutral sequences. Satsuma does not require any pre-processing, such as repeat masking, since it will automatically detect ambiguous mappings.

Satsuma has parallelization built-in and is designed to run on multi-core architectures. The run-time for aligning two bird-size genomes (~1.2 Gb) is around two days on 24 CPUs.

You can find the manual here.
Download the latest source code from here.
Stable versions can also be downloaded from the Broad Institute's web site.

An incomplete list of questions and answers (yes, these have really been asked by our users! Please feel free to add your own by e-mailing us) is here.

If you use Satsuma in your research, please cite:
Grabherr, M. G., Russell, P., Meyer, M., Mauceli, E., Alföldi, J., Di Palma, F., & Lindblad-Toh, K. (2010). Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics, 26(9), 1145-51.

Tutorial at http://evomics.org/learning/genomics/satsuma/

Address of the bookmark: http://satsuma.sourceforge.net/

Hagfish - assess an assembly through creative use of coverage plots

Abhi — Fri, 20 May 2016 19:08:17 -0500

Hagfish is a tool that is to be used in data analysis of Next Generation Sequencing (NGS) experiments. Hagfish builds on the concept of coverage plots and aims to assist (amongst others) in quality control of de novo genome assembly or identification of structural variation in a genome re-sequencing experiment.

Hagfish requires a reference sequence and a paired end re-sequencing data set. Hagfish has more power the larger the insert size of the paired end library is.

Quick links: Installation,Operation, Read mappers, Hagfish scripts, Hagfish plots

Address of the bookmark: https://github.com/mfiers/hagfish

Bpipe - a tool for running and managing bioinformatics pipelines

Radha Agarkar — Sat, 21 May 2016 22:42:16 -0500

Bpipe provides a platform for running big bioinformatics jobs that consist of a series of processing stages - known as 'pipelines'.

January 20th, 2016 - New! Bpipe 0.9.9 released!
Download latest, all
Documentation
Mailing List (Google Group)

Bpipe has been published in Bioinformatics! If you use Bpipe, please cite:

Sadedin S, Pope B & Oshlack A, Bpipe: A Tool for Running and Managing Bioinformatics Pipelines, Bioinformatics

Address of the bookmark: http://docs.bpipe.org/

Stand-alone programs for Bioinformatician

Radha Agarkar — Sat, 21 May 2016 22:50:15 -0500

This directory contains applications for stand-alone use, built specifically for a Linux 64-bit machine.

For help on the bigBed and bigWig applications see:
http://genome.ucsc.edu/goldenPath/help/bigBed.html
http://genome.ucsc.edu/goldenPath/help/bigWig.html

View the file 'FOOTER' to see the usage statement for each of the applications.

Address of the bookmark: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

Research Associate Bioinformatics at MANIT

Thu, 26 May 2016 02:20:58 -0500

Research Associate Jobs opportunity in Maulana Azad National Institute of Technology (MANIT) on contract basis
Project : “Screening of Anti-venom potential of medicinal plants from Tribal region of Madhya Pradesh"
No. of Post : 01

Qualification : The minimum qualifications are : Ph.D in Bioinformatics/ Biotechnology or allied branches with atleast two publication in SCI journals.
Fellowship : The consolidated emoluments of Rs.36, 000/ PM+HRA+MA as per CSIR rules.

How to apply
Applications (in prescribed attached format and supporting documents) to be received in the Dr. Rahul Shrivastava, Principal Investigator (CSIR Project), Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal – 462003 (MP) on or before 7th June 2016.

More at http://www.web.manit.ac.in/Year%202016/Recruitment%20Contract%20Faculty/Biological/Advertisement%20for%20Antivenome%20project%202.pdf

BioDBnet

Jit — Thu, 02 Jun 2016 11:11:47 -0500

Database to Database Conversions

db2db allows for conversions of identifiers from one database to other database identifiers or annotations. To use db2db select the input type of your data, changing the input type automatically changes the output options to the ones specific for the input selected. Then select one or more output types and add your identifiers in the ID list box. Set the remove duplicate values to 'No' if you do not want duplicates to be removed. Clicking on submit then returns a table of your inputs matched against all the outputs selected in the exact order as entered. Results can be limited to a particular taxon by entering it's Taxon ID. The performance will vary widely depending on the number of outputs and the options selected. Conversions to a single output with the default options should complete in a few seconds

Address of the bookmark: https://biodbnet-abcc.ncifcrf.gov/db/db2db.php

Assistant Professor Bioinformatics / Teaching Assistant at Gujarat University

Sat, 04 Jun 2016 16:04:26 -0500

Assistant Professor Bioinformatics / Teaching Assistant Jobs recruitment in Gujarat University
Departments :

M.Sc. Bioinformatics Climate Change and Impacts Management
M.Sc. Biotechnology and Clinical Research

Department of Computer Science (Rollwala Computer Centre)
Appointment will be on purely contract basis for 11 months on consolidated salary. Reservation as per rules

How to apply
All the candidate are here by required to fill up the application form and given to concern Department, Gujarat University, Ahmedabad (Form can be submitted personally or thorough post/courier.) Candidates are supposed to attach the self attested photocopies of their required testimonials along with application form. Last date of receipt of application is 10/06/2016.

More http://www.gujaratuniversity.org.in/web/NWD/NewsEvents/1700_Recruitments%20at%20Gujarat%20University.asp

clusterProfiler

Jit — Thu, 16 Jun 2016 18:57:03 -0500

statistical analysis and visulization of functional profiles for genes and gene clusters

Bioconductor version: Release (3.3)

This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

Author: Guangchuang Yu with contributions from Li-Gen Wang and Giovanni Dall'Olio.

Maintainer: Guangchuang Yu

Citation (from within R, enter citation("clusterProfiler")):

Yu G, Wang L, Han Y and He Q (2012). “clusterProfiler: an R package for comparing biological themes among gene clusters.” OMICS: A Journal of Integrative Biology, 16(5), pp. 284-287.
Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("clusterProfiler")

https://www.bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html

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

Machine Learning !!!

Gudiya Pal — Fri, 01 Jul 2016 12:57:12 -0500

In machine learning, computers apply statistical learning techniques to automatically identify patterns in data. These techniques can be used to make highly accurate predictions.

Keep scrolling. Using a data set about homes, we will create a machine learning model to distinguish homes in New York from homes in San Francisco.

Address of the bookmark: http://www.r2d3.us/visual-intro-to-machine-learning-part-1/