How Do I Install and Use Bioperl on Ubuntu 14.04.1 LTS

Bioperl is necessary to run several Perl script which can save your day. Although Perl already comes with Ubuntu but Bioperl should be install manually. I tried to install Bioperl following the instruction given on the official page of Bioperlon my Ubuntu 14.04.1 LTS but it always ends with error. Then I realised that I can directly download the Bioperl from Ubuntu packages by typing a simple command. Even I don't have to go through CPAN. I also share methods th install Bioperl on Windows mechine HERE. Just type this command in your terminal and you are done. So this is the easiest way to install the Bioperl ever
sudo apt-get install bioperl
Simply run this Perl script in your terminal. If it end without any error then you are set.
#!/bin/perl -w
 
use Bio::Seq;
Finally, How to install a new Perl module? Is it also very easy. Just type a simple command in your terminal and done
cpan Bio::Seq
Here Bio::Seq is is the name of Perl module I want to install. You can replace it with whatever Perl module name you want to install.
Note to me
It is not necessary but you may have to add these module to your path
bp_aacomp, bp_biblio, bp_biofetch_genbank_proxy, bp_bioflat_index, bp_biogetseq, bp_blast2tree, bp_bulk_load_gff, bp_chaos_plot, bp_classify_hits_kingdom, bp_composite_LD, bp_das_server, bp_dbsplit, bp_download_query_genbank, bp_einfo, bp_extract_feature_seq, bp_fast_load_gff, bp_fastam9_to_table, bp_fetch, bp_filter_search, bp_flanks, bp_gccalc, bp_genbank2gff, bp_genbank2gff3, bp_generate_histogram, bp_heterogeneity_test, bp_hivq, bp_hmmer_to_table, bp_index, bp_load_gff, bp_local_taxonomydb_query, bp_make_mrna_protein, bp_mask_by_search, bp_meta_gff, bp_mrtrans, bp_mutate, bp_netinstall, bp_nexus2nh, bp_nrdb, bp_oligo_count, bp_pairwise_kaks, bp_parse_hmmsearch, bp_process_gadfly, bp_process_sgd, bp_process_wormbase, bp_query_entrez_taxa, bp_remote_blast, bp_revtrans-motif, bp_search2BSML, bp_search2alnblocks, bp_search2gff, bp_search2table, bp_search2tribe, bp_seq_length, bp_seqconvert, bp_seqfeature_delete, bp_seqfeature_gff3, bp_seqfeature_load, bp_seqret, bp_seqretsplit, bp_split_seq, bp_sreformat, bp_taxid4species, bp_taxonomy2tree, bp_translate_seq, bp_tree2pag, bp_unflatten_seq 

Extract Part of a FASTA Sequences with Position by python script HERE

How Do I Install and Use RepeatMasker

Why Did I Use RepeatMasker

Actually, RepeatMasker 'is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. So RepeatMasker take the sequences and compare them to a repeat library and finally replace the repeats in your query with 'N'or other non DNA bases.

Dependencies

  1. Unix system with perl
  2. TRF - Tandem Repeat Finder DOWNLOAD
  3. Sequence Search Engine  RMBlast DOWNLOAD
  4. Repeat Database DOWNLOAD : You need to open an account. Approval of account may take couple of days.
  5. RepeatMasker DOWNLOAD

Installation

  1. Unpack all softwares
  2. Copy TRF - Tandem Repeat Finder, RMBlast, makeblastdb and blastx exceutibles in RepeatMasker bin directory
  3. Rename Tandem Repeat Finder to trf
  4. In linux terminal, go to the bin directory of Repeatmasker and run
    perl ./configure
    
  5. This massage will appear in terminal
    RepeatMasker Configuration Program
    
    This program assists with the configuration of the
    RepeatMasker program.  The next set of screens will ask
    you to enter information pertaining to your system
    configuration.  At the end of the program your RepeatMasker
    installation will be ready to use.
    
    
    
    <PRESS ENTER TO CONTINUE>
    
    Now press enter
  6. This massage will appear in terminal
    **PERL PROGRAM**
    
      This is the full path to the Perl interpreter.
      e.g. /usr/local/bin/perl or enter "env" if you prefer to use
      the "/usr/bin/env perl" mechanism to locate perl.
    Enter path [ /usr/bin/perl ]:
    
    Now installer will search for PERL installation location. If it is different from above given path, then give the correct path for PERL to installer and press the enter.
  7. This massage will appear in terminal
    **REPEATMASKER INSTALLATION DIRECTORY**
    
      This is the path to the directory where
      the RepeatMasker program has been installed.
    
    Enter path [ /home/sanjay/Desktop/RepeatMasker ]:
    
    Now installer will search for RepeatMasker directory location. If it is different from above given path (I have extracted the downloaded RepeatMasker file on deskop), then give the correct path for RepeatMasker to installer and press the enter.
  8. This massage will appear in terminal
    **TRF PROGRAM**
    
      This is the full path to the TRF program.
     This is now used by RepeatMasker to mask simple repeats.
    
    Enter path [  ]:
    
    Now installer will search for Tandem Repeat Finder directory location. Since i have already copied the Tandem Repeat Finder in RepeatMasker directory therefore i will just copy the RepeatMasker directory path that is '/home/sanjay/Desktop/RepeatMasker' for me. If it is different from above given path , then give the correct path for Tandem Repeat Finder to installer and press the enter.

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