How To Perform Basic Multiple Sequence Alignments In R

There are several servers out there to perform the multiple sequence alignment and visualization. I was looking for all in one offline tool to perform the multiple sequence alignment and generate a publication quality image. We can use msa package for both amino acid and DNA alignment. Following Rscript can be used for this purpose. Script is heavily commented to easy understand.Hope it will be helpful for others too.

Sequence Similarity Search - I : Basic Local Alignment Search Tool (BLAST) HERE

Easiest Way to Download All Sra Samples or Multi Experiment file from NCBI SRA database

European Nucleotide Archive is good place to start to download the raw fastq files. But it is not easy to download multiple run files from NCBI SRA database. I recently learn to download in relatively easy way. I want to download these four run together from NCBI SRA database : SRR122247,SRR122248,SRR122249, SRR122250. Format of basic url is like that{SRR|ERR|DRR}/<first 6 characters of accession>/<accession>/<accession>.sra
Where {SRR|ERR|DRR} should be either ‘SRR’, ‘ERR’, or ‘DRR’ and should match the prefix of the target .sra file Described in details HERE. So my final urls will look like this
Now save this urls in a text file (url_list.txt, for example). Run the wget like this
wget -i url_list.txt
run sudo apt-get install wget from terminal if you don't have wget

Journal Citation Reports 2015 / 2016

Recently, Thomson Reuter announced Journal Citation Reports® for year 2016. Actually Journal Citation Reports® offers a systematic means to critically evaluate the world's leading journals, with quantifiable, statistical information based on citation data by compiling articles' cited references. Thus in scientific community journal impact is now considering as a quality measure of published work. JCR is actually contains the journal impact factor, number of times they cited in different journals and other statistical values. So this list of journal impact factors is made by the data gathered throughtout 2015 that is why you can also say it journal impact factor 2015 download. You can view this SCI journal impact factor 2015  in other tab by clicking HERE or you can download journal impact factor 2015 HERE

How to download only viridiplantae miRNA from miRBase

There is no direct way to download the organism specific miRNA from miRBase database. So I extracted the miRNA of viridiplantae plant from miRBase using some unix command. Steps are as follows
  •  Download the information regarding organisms from HERE.
  • Download the mature miRNA sequence from HERE
  • Extract both files in same directory
  • Download the fasta dereplicating python script from HERE
  • Now run the bash script given from the same directory
  • #!/bin/bash
    #script to extact plant mirna from mirbase database
    # convert fasta to tab
    awk 'BEGIN{RS=">"}{gsub("\n"," ",$0); print ">"$0}' mature.fa >
    #extract the organisms belong to Viridiplantae. You can extract the miRNA for other
    # organism too by changing the word "Viridiplantae"
    grep Viridiplantae organisms.txt >plants_mirbase.txt
    # extract name of plants
    awk '{ print $3 " " $4 }' plants_mirbase.txt >plant_name.txt
    #extract mirna for plants
    grep -f plant_name.txt >
    #convert tab to fasta
    awk '{print ""$1" "$2" "$3" "$4" "$5"\n"$6}' > plant_mirna.rna
    #convert RNA to DNA
    sed '/^[^>]/ y/uU/tT/' plant_mirna.rna  >plant_mirna.fasta
    #dereplicate mirna file
    python -i plant_mirna.fasta
    #cleaning fasta header
    cat derep_plant_mirna.fasta | awk -F ';' '{print $1}' >plant_mature_mirna_unique.fasta
    rm plants_mirbase.txt
    rm plant_mirna.rna
    rm plant_name.txt
    rm derep_plant_mirna.fasta
    echo mature mirna from all plants are in plant_mirna.fasta!!!
    echo unique mature mirna from all plants are in plant_mature_mirna_unique.fasta!!!
    echo all job done!!!
Basically the above bash script extract the miRNA from plant deposited to miRBase database and save them to a file plant_mirna.fasta. In second part, it remove the duplicate miRNAs and save them in another file plant_mature_mirna_unique.fasta.
How to remove duplicate sequences from FASTA file HERE

BLAST Database creation error