Question: Get BUSCO gene descriptions
2
gravatar for pbigbig
3.2 years ago by
pbigbig190
United States
pbigbig190 wrote:

Hi everyone,

I am planning to design primers (to run Sanger sequencing) for assessment of a genome de novo assembly. These primers can be chosen arbitrary, but I prefer to have some meaning of sequenced results, therefore I run BUSCO eukaryote (~400 single-copy orthologs) on the de novo assembly genome. BUSCO run revealed ~60% Complete Single-Copy BUSCOs, but I wonder how could I get to know the name and description of those orthologs in eukaryote set (there are only alignments and numbered code for matches in results)? I really appreciated any help.

Thank you very much in advance.

Phuong.

busco de novo assembly • 1.7k views
ADD COMMENTlink modified 6 months ago by william.imart0 • written 3.2 years ago by pbigbig190

Also very interested in this, have you found an answer?

ADD REPLYlink written 2.9 years ago by twooldridge0

Sadly not yet, but I could still obtain those ortholog's fasta sequences in BUSCO results and Blast them against Refseq database to get best hit accession ID, then simply refer list of these IDs for descriptive titles (I used Batch Entrez http://www.ncbi.nlm.nih.gov/sites/batchentrez)

ADD REPLYlink written 2.9 years ago by pbigbig190
0
gravatar for william.imart
6 months ago by
william.imart0 wrote:

If you load the FASTA sequence into IGV you can look at the entire genome alongside the genes they code for. From there you can search the name and function of each of these genes.

ADD COMMENTlink written 6 months ago by william.imart0
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