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2 hours ago by

Hi everyone

I am new in this topic I am trying to perform a local blast analysis using the cmd of windows 10 (could be not the best but I am not familiarized with Linux and learn to use it from my windows pc could take me a long time so if I can do it in windows that that would save me time)

  • So I started to downloading the blast+ program from NCBI and create the environment variables.
  • I downloaded my protein query in fasta format (I have 50 of them)
  • I downloaded 15 transcriptome codes from another source (because is not available in NCBI). they are in fasta format, each one has 5GB.
    -After I created my database from my transcriptome fasta format using makeblastdb

    makeblastdb -in sp1.fasta -dbtype nucl -title espone

Now I ran a blastn analysis with one of my proteins querys (fasta format) using one of my databases (named:spone).

blastn.exe -query protein1.fasta  -outfmt 6 -db spone -out test.txt

the result was:

 FASTA-Reader: Ignoring invalid residues at position(s): On line 2: 7, 9, 15, 21, 25-26, 30-33, 36-38, 43, 50, 52-53, 60-61, 64-68
FASTA-Reader: Ignoring invalid residues at position(s): On line 3: 9, 14-15, 19, 22, 25, 33-34, 40, 47, 53-55, 60, 62-63, 65-66, 69
FASTA-Reader: Ignoring invalid residues at position(s): On line 4: 4, 6, 12-15, 26, 31-32, 36, 39-40, 43, 50-51, 56, 65, 67

Here begin my problems:

  • The out result (test.txt) is empty has 0 Kb... Why is happening this?
  • I have 50 proteins (query) and I need to run blast analysis of all of them in the transcriptome of the 15 species so I would like to know if there is some method to run my 50 query in my 15 transcriptome database at the same time.
  • I need that the result shows me the taxonomic names of each specie (15) and the name of proteins (50). For that I downloaded taxdb but I am not sure how this works.
  • If It is possible I would like to know the best form to visualise the data (using a bridge between cmd result and e.g. R).

By the way, I have 16 BG in RAM ITB of SSD just for programs and ITB HD. (I hope that my laptop capacity does not a problem).

I know that is a lot of questions but I tried to find tutorials but I could not find anything precise.
Thanks in advance for your help.

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