I have sequenced a bacteriophage (after CsCl purification and DNA extraction) and assembled the paired ends. The assembled .contig file is a multi FASTA file with many nucleotide sequences (of varying node length and coverage). what does the multi-sequences mean? How to process this file further to identify the bacteriophage? similarly, how to know that the sequence is not contaminated?
I have attached a screenshot of the sequences for reference.
There are several tool for this purpose and you can easily find that with a simple keyword search in your browser. However, if you don't know much about bioinformatics, you can simply use the online servers which can do the job for you. Use PHAST or PHASTER. Here you can simply upload file and get the final results.
Regarding your question about what is multiple sequence? That is what you call a multi fasta file.
If you want to know if there is any contamination, first you need to define and fix your definition of contamination. And based on your data processing you might be able to get some answer.
Abhijeet Singh Thanks for the response. yes, I am basically amateur at bioinformatics. I did try uploading the multi fasta file on PHASTER and PATRIC. The result I got did not make any sense to me ( as I am very new to gene Phage genomics studies). Basically what I want is to identify the bacteriophage. I have the sequenced genome. What I want next is to identify whether there is any foreign genomic contamination (contamination of genes from other than the original bacteriophage for say, bacterial, human, etc). How can I identify whether the bacteriophage is novel or not?
Get help of some colleague your supervisor or someone, who knows something about bioinformatics or phage biology.
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