SEA-PHAGES | All posts created by balish

Link to this post \| posted 21 Mar, 2019 15:25
balish	One of my students asked me about something that I too have noticed before, but I don't really understand it. Occasionally, for a given amino acid sequence, the BLAST scores on DNA Master don't match up correctly with the actual alignment data. This often seems to happen when the alignment includes low-complexity regions (marked by a string of X's in the alignment). The current example we're working with is that DNA Master returns a score of 194 for the alignment between Belthelas 20 and its homolog in BurtonThePup, with two mismatches, both in a low-complexity region. On the other hand, the alignment between Belthelas 20 and its homolog in VitualEligans, which are 100% identical, results in a score of only 186. It seems as though BLAST can lead us to compare our protein of interest to a protein that isn't the most similar one. What's going on here, and how do we deal with it?

Link to this post | posted 21 Mar, 2019 15:25

One of my students asked me about something that I too have noticed before, but I don't really understand it. Occasionally, for a given amino acid sequence, the BLAST scores on DNA Master don't match up correctly with the actual alignment data. This often seems to happen when the alignment includes low-complexity regions (marked by a string of X's in the alignment). The current example we're working with is that DNA Master returns a score of 194 for the alignment between Belthelas 20 and its homolog in BurtonThePup, with two mismatches, both in a low-complexity region. On the other hand, the alignment between Belthelas 20 and its homolog in VitualEligans, which are 100% identical, results in a score of only 186. It seems as though BLAST can lead us to compare our protein of interest to a protein that isn't the most similar one. What's going on here, and how do we deal with it?

Posted in: Annotation → BLAST score algorithm

Link to this post \| posted 30 Jan, 2019 19:09
balish	One of my students this semester has a Chromebook. Will it be possible for her to install and run DNA Master, and if so, how?

Posted in: DNA Master → DNA Master and Chromebook

Link to this post \| posted 26 Apr, 2018 16:04
balish	Thanks, that's very helpful!

Posted in: Functional Annotation → Pham 37120

Link to this post \| posted 25 Apr, 2018 18:07
balish	There are some genes/proteins out there that have two or more completely different annotations depending on which phage you’re in, undoubtedly resulting from propagation of errors. I don’t want to continue to propagate those errors. Pham 37120 proteins (from M. smeg phages) are sometimes annotated as "tail protein" and sometimes as "terminase, small subunit." Interestingly, they have very significant BLAST hits to genes in the chromosomes of many Actinobacteria, and they don’t match any gene annotated as either a terminase or a tail protein from any phages other than the ones from within the SEA-PHAGES program. Taken together, the features of this gene don’t strike me as being consistent with either ascribed function, although anything is possible. It seems to me that it’s a gene that was picked up from a host a long time ago and has been carried around ever since. It's also closely related to genes in other Phams, like 37118, so it's even more widespread than it appears simply based on the number of genes in the Pham. So what is the function of this protein? What's the correct annotation? I’m copying the amino acid sequence from Magnar’s Pham 37120 protein. MGTRGPIPNRSDERVRRNKEEYGEVTTLPVSGPVKSPPLGLTDPHPIVRDLYNSLAESAQAALYQPSDWSYAKFTLHFADQLLKKSDPSAMMLATVNQMLSSLLVSEGDRRRVRIEVERTKSDGPDASVTTMGELFERALRKPKSS Best, Mitch Edited 25 Apr, 2018 18:08

Link to this post | posted 25 Apr, 2018 18:07

balish

There are some genes/proteins out there that have two or more completely different annotations depending on which phage you’re in, undoubtedly resulting from propagation of errors. I don’t want to continue to propagate those errors.

Pham 37120 proteins (from M. smeg phages) are sometimes annotated as "tail protein" and sometimes as "terminase, small subunit." Interestingly, they have very significant BLAST hits to genes in the chromosomes of many Actinobacteria, and they don’t match any gene annotated as either a terminase or a tail protein from any phages other than the ones from within the SEA-PHAGES program. Taken together, the features of this gene don’t strike me as being consistent with either ascribed function, although anything is possible. It seems to me that it’s a gene that was picked up from a host a long time ago and has been carried around ever since. It's also closely related to genes in other Phams, like 37118, so it's even more widespread than it appears simply based on the number of genes in the Pham.

So what is the function of this protein? What's the correct annotation? I’m copying the amino acid sequence from Magnar’s Pham 37120 protein.

MGTRGPIPNRSDERVRRNKEEYGEVTTLPVSGPVKSPPLGLTDPHPIVRDLYNSLAESAQAALYQPSDWSYAKFTLHFADQLLKKSDPSAMMLATVNQMLSSLLVSEGDRRRVRIEVERTKSDGPDASVTTMGELFERALRKPKSS

Best,
Mitch

Edited 25 Apr, 2018 18:08

Posted in: Functional Annotation → Pham 37120

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