Question: How to find which genes are missing?
0
gravatar for guardsquirrel
12 months ago by
guardsquirrel0 wrote:

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.

ADD COMMENTlink modified 5 months ago by Mensur Dlakic6.6k • written 12 months ago by guardsquirrel0
2
gravatar for Mensur Dlakic
5 months ago by
Mensur Dlakic6.6k
USA
Mensur Dlakic6.6k wrote:

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.

ADD COMMENTlink written 5 months ago by Mensur Dlakic6.6k

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

ADD REPLYlink written 5 months ago by Bioinfo20
2

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

ADD REPLYlink modified 5 months ago • written 5 months ago by genomax89k

Ahhh very clear, Thank you very much for you answer

ADD REPLYlink written 5 months ago by Bioinfo20
1
gravatar for Rashedul Islam
11 months ago by
Canada
Rashedul Islam370 wrote:

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.

ADD COMMENTlink written 11 months ago by Rashedul Islam370
1

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

ADD REPLYlink written 5 months ago by genomax89k
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