SEA-PHAGES | All posts created by neitzelj

Link to this post \| posted 02 Mar, 2021 19:46
neitzelj	Another paper on r genes: https://www.genetics.org/content/genetics/148/4/1539.full.pdf

Posted in: Functional Annotation → riiA and riiB like proteins

Link to this post \| posted 19 Jul, 2018 16:43
neitzelj	Welkin Pope Hi Jim, Those strings of Xs are the result of a low-complexity sequence filter that BLAST has which is enabled in DNA Master. Unfortunately, there is no way to turn it off in the program, but you can redo the search on the NCBI website with the filter off if you want. Best, Welkin Thanks for the explanation. Fortunately the filter often seems to leave the N-termini intact so for start sites it is fine, and I do usually do the NCBI version to confirm functions. -Jim

Link to this post | posted 19 Jul, 2018 16:43

neitzelj

Welkin Pope
Hi Jim,
Those strings of Xs are the result of a low-complexity sequence filter that BLAST has which is enabled in DNA Master. Unfortunately, there is no way to turn it off in the program, but you can redo the search on the NCBI website with the filter off if you want.
Best,
Welkin

Thanks for the explanation. Fortunately the filter often seems to leave the N-termini intact so for start sites it is fine, and I do usually do the NCBI version to confirm functions.
-Jim

Posted in: DNA Master → Odd BLAST results via DNAMaster

Link to this post \| posted 19 Jul, 2018 16:29
neitzelj	In running some BLAST results on genes in DNAMaster, in some cases when the matches are shown amino acids in the query are converted to strings of XXXXs as unknowns. This usually seems to happen in the region around 50 AAs into the protein, which makes using these results a bit problematic. More puzzling is that this seems to be kind of a random outcome, which happens to a handful of searches but is not a general occurrence. Any ideas about why this is happening? -Jim Neitzel

Link to this post | posted 19 Jul, 2018 16:29

neitzelj

In running some BLAST results on genes in DNAMaster, in some cases when the matches are shown amino acids in the query are converted to strings of XXXXs as unknowns. This usually seems to happen in the region around 50 AAs into the protein, which makes using these results a bit problematic. More puzzling is that this seems to be kind of a random outcome, which happens to a handful of searches but is not a general occurrence. Any ideas about why this is happening?
-Jim Neitzel

Posted in: DNA Master → Odd BLAST results via DNAMaster

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