how do i install Blast2go on Ubuntu


What is Blast2Go 

Blast2go is a software tool for the automated, high-throughput functional annotation of novel sequence. Blast2go use BLAST to identify similar sequences and then transfers existing functional annotation from hits to query sequences.

Requirements



  • Webstart file from HERE 
  • JAVA enabled machine 

  • How to run Blast2go on Ubuntu

    Although Ubuntu come with its own java version but I found that it didn't work for Blast2go. Therefore I decide to install Oracle Java (JDK). You can install Oracle Java (JDK) by these commands one by one
    sudo add-apt-repository ppa:webupd8team/java
    sudo apt-get update
    sudo apt-get install oracle-java8-installer
    You can your java version by this command
    java -version
    it should print like this in terminal
    java version "1.7.0_67"
    Java(TM) SE Runtime Environment (build 1.7.0_67-b01)
    Java HotSpot(TM) 64-Bit Server VM (build 24.65-b04, mixed mode)
    
    Note to me
    Above command will install  Oracle Java 8 but I found that Blast2go didn't work for Oracle
     Java 8 therefore I decide to install previous  version of Oracle Java. You can replace 8 with 
    6 or 7 to install Oracle Java 6 or Oracle Java 7 
    
    Now we are all set. Just go to your working directory and type
    javaws blast2go1000.jnlp
    Remember that I downloaded the 1000MB version of Blast2go therefore my command include the '1000'. It should as per your requirement.

    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 
    

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