Hi Dear ones
I have got a FASTA file of the whole-genome sequence of bacteria. it is containing more than 30000 contigs, the first initial contigs are very big in size (1-4 million bp) and END contigs are very small (few hundreds) only.
I have two questions to ask.
Q1. Containing 30000 contigs may be providing good data? as I came to know contigs number should be small within few hundreds.
Q2. I need to do mapping, annotation and further analysis (using OMICS software) with this FASTA file, for this I need to download XML2 by blasting at blastX in NCBI, but blastX can take up to 30-40 thousands bases only. so need to know how to do blastX in NCBI for very large contigs. please give suggestions and help. thank you
Mohan Kumar Verma Your 30000 contigs may represent more than one bacterial genome. You can make a BLAST for 16S rRNA gene against your data to show that you have one bacterium or more.
- I would highly recommend to check what data you get as a genome sequence. Does not look like a good genome sequence thus moving forward with that data, in my opinion, could be a waste of time.
Hi Vipin
Use either The Genome Taxonomy Database (GTDB) or RAST (Rapid Annotations using Subsystems Technology) toolkit.
If its a bacterial genome use the above tools
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