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How to find which genes are missing?

Hi everyone, I've made an assembly for a chloroplast genome, however I'm confused as to what I have to do next...

I'm trying to identify any genes that are normally present in chloroplasts but are missing in my assembly. How could I go about doing this?

Thank you so much.

assembly genome chloroplast alignment gene
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updated by Mensur Dlakic Mensur Dlakic • written by guardsquirrel • guardsquirrel

2 answers

It should not be very difficult to do this assuming that you have basic familiarity with running BLAST from the command line.

  • create a FASTA database of genes (or proteins) normally present in chloroplasts
  • create a FASTA database of genes (or proteins) in your assembly
  • create a BLASTn (or BLASTp, if proteins) database of your sequences
  • use BLASTn (or BLASTp, if proteins) to search all sequences from the first step versus the database created in the third step

Any gene (or protein) that doesn't have a match is missing in your assembly.

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written by Mensur Dlakic Mensur Dlakic

Hello , please i was asking the same thing and i think your answer is soo good to solve this , just i didn't undrestand the first 4 , what you mean create a BLASTn (or BLASTp, if proteins) database of your sequences ?? how can you do that ? , Thank you

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written by Bioinfo • Bioinfo

You would create the blast databases using makeblastdb. Spend some time with "getting started manual" from NCBI for a quick intro.

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written by GenoMax GenoMax

Ahhh very clear, Thank you very much for you answer

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written by Bioinfo • Bioinfo

If I understand you question correctly - you want to get the genes that are not present in known chloroplasts genomes and you have the assembled genes of the chloroplast genome of your interest.

For that you can use blastn.

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written by Rashedul Islam Rashedul Islam

OP was asking to identify any genes that are normally present in chloroplasts but are missing in my assembly.

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written by GenoMax GenoMax

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