• Intro

  • step_01
  • step_02
  • step_03
  • step_04
  • step_05
  • step_06
  • step_07
  • step_08
  • step_09
  • step_10
  • step_11
  • step_12
  • step_13
  • step_14
  • step_15
  • step_16
  • step_17
  • step_18
  • step_19
  • step_20
  • step_21
  • step_22
  • step_23
  • step_24

  • Credits

    UC Davis

    Step 4: BLAST search to reduce number of ESTs for CAP3 assembly

    Only ESTs of different genotypes that produced BLAST hits to each other were selected for CAP3 assembly. In other words: we are not interested in singletons. With this step we reduce the number of ESTs in our dataset which makes obtaining of CAP3 assembly results faster and with fewer requirements for computer memory.

    [Note, this step is not required if your dataset contains less than ~50,000 ESTs]

    We have run BLASTN two times:

    Lycopersicon_hirsutum.fasta against Lycopersicon_esculentum.fasta
    Lycopersicon_pennellii.fasta against Lycopersicon_esculentum.fasta

    Following commands were executed using stand-alone NCBI BLAST program:

    $ formatdb -i Lycopersicon_esculentum.fasta -p F -o T

    $ blastall -p blastn -F T -d ./Lycopersicon_esculentum.fasta -i ./Lycopersicon_hirsutum.fasta -o ./Lycopersicon_hirsutum_vs_Lycopersicon_esculentum.blastn -e 1e-20 -v 24 -b 24 -I T &

    $ blastall -p blastn -F T -d ./Lycopersicon_esculentum.fasta -i ./Lycopersicon_pennellii.fasta -o ./Lycopersicon_pennellii_vs_Lycopersicon_esculentum.blastn -e 1e-20 -v 24 -b 24 -I T &

    It takes several hours to finish BLASTN run with these datasets.