Hello,
I have sequencing data of cattle blood plasma and data was BLAST with nr/nt database. In resulting file i counted the number of sequence present in different genus. Further selected three organisms for study; 1. Babesia bigemina 2. Gongylonema pulchrum 3. Wuchereria bancrofti, then assembled the reads of above organisms with genome in CLC platform and extracted only consensus sequences. Performed NCBI BLAST with nr/nt database of extracted consensus sequences.
Result obtained after BLAST showed like 1. Babesia bigemina query length is 2107, it gives 100% query cover and 98% identity with Babesia bigemina; but also 98% query cover and 99% identity between phylum like, bovine, Clostridium botulinum, Ovis canadensis canadensis, Gongylonema pulchrum, Wuchereria bancrofti, Bison bonasus; they cover more than 800-1000 bases. i tried BLASTx, pfam, interpro, BLASTp for finding the annotation of aligned regions in different organisms, but not showing any information for cover sequence. Babesia bigemina showed like hypothetical protein-conserved, in other cases not showing any annotation regions. so, i am trying to find the sequence which highly cover at phylum level, is it domain or conserved part?
Is the blood plasma sequenced after a particular treatment? Can you find the sources of the reference sequences that your query is blasting to? Makes me think if it is a novel protein that is specific to a treatment or sample. I have a similar situation with an insect salivary protein and is found in only another closely related insect but has no annotation in any of the databases.
Hi Nimita,
This type of cross kingdom conservation is very interesting and would be unusual even for structural vs. coding RNA regions. Was your original data from a DNA or RNA sequencing project? Did you limit your NCBI blast search to the RefSeq database?
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