Link to this post | posted 29 Mar, 2019 13:10
jawsWPI	Hi Debbie, This actually was quite helpful, and for now I will be probably be assigning these as NKF. But it may form the basis for an senior thesis project I will be co-advising next year with Mike Buckholt. Thanks!

Link to this post | posted 28 Mar, 2019 20:41

jawsWPI

How long does a membrane protein need to be? I have run into a couple of cases where the protein is very small (30-45ish aa) and has one transmembrane domain, called by both TmHmm and SOSUI. Or are these better left as NKF? Here's an example: From TmHmm: # WEBSEQUENCE Length: 43 # WEBSEQUENCE Number of predicted TMHs: 1 # WEBSEQUENCE Exp number of AAs in TMHs: 19.16541 # WEBSEQUENCE Exp number, first 60 AAs: 19.16541 # WEBSEQUENCE Total prob of N-in: 0.01540 # WEBSEQUENCE POSSIBLE N-term signal sequence WEBSEQUENCE TMHMM2.0 outside 1 4 WEBSEQUENCE TMHMM2.0 TMhelix 5 24 WEBSEQUENCE TMHMM2.0 inside 25 43 From SOSUI This amino acid sequence is of a MEMBRANE PROTEIN which have 1 transmembrane helix. No. N terminal transmembrane region C terminal type length 1 4 VLFVLDLHIVALGLLSWFCLVCD 26 PRIMARY 23

Link to this post | posted 26 Mar, 2019 15:15
jawsWPI	Lokk gene 36 (26423 - 27289 ) | pham 23651 Rachaly_Draft gene 36 (26457 - 27356 ) | pham 23651 Both are reverse genes. Right now there are only 5 members in the pham; two subclusters (A2 and A14); Lokk and CRB1 are the only non-draft genomes. Edited 26 Mar, 2019 15:24

Link to this post | posted 26 Mar, 2019 13:42

jawsWPI

What current official function should be assigned to this pham in Rachaly and other drafts? Lokk has called it a “DNA binding domain protein”, CRB1 calls it a putative Rep protein. The research I have done suggests a best fit to “helix-turn-helix DNA binding domain". I know that Debbie (et.al.?) were going to start investigating this gene and the Par system genes in Lokk and Rachaly back in 2017. Do you have any results that would give us the answer to this question?

Link to this post | posted 15 Mar, 2019 14:36

jawsWPI

The blast and HHPred evidence suggests that Anakin and NarutoRun's gene 16 (also gene 16 in AnnaSerena and Krampus) is the scaffolding protein–see attached document. AnnaSerena and Krampus assign this as NKF. The synteny is almost correct: it precedes the major capsid, BUT there is an intervening NKF gene; all of these gene are in phams that only belong to EF. The question is: is this intervening NKF gene enough to disqualify assigning scaffolding protein as the gene 16 function? (I have been told that the scaffolding protein usually immediately precede the major capsid.) 233Kb

Link to this post | posted 13 Mar, 2019 15:09
jawsWPI	After some additional digging there is no substantial evidence for two domains in the alpha chain. So, I'm going to continue the trend and leave these two gene calls with the same function. Thanks!

Link to this post | posted 08 Mar, 2019 22:03

jawsWPI

I'm working on two EF draft genomes. All 7 EF genomes have a DnaE-like DNA polymerse III (alpha) "gene" that has been split into two parts. These are genes 56 and 57 in Anakin and NarutoRun, the genes are coding from different frames (+1 and +2), gene 57's RBS Z score is 2.415 it has a so-so final score of -4.264, and there is a consistent 11 bp gap between the genes. The non-draft genomes AnnaSerena and Krampus give both genes the same DnaE-like DNA polymerse III (alpha) function. In an HHPred anaylsis Gene 56 aa1 - 315 has a 100% probability match to aa 19-324 of an Ecoli DnaE DNA polymerase III (alpha) crystal structure, and gene 57 aa15-594 matches (100% probability) the Ecoli structure from 315 - 1160. (If I run HHPred with the merged gene56+57 sequence I again get a 100% probability match but now to the full length Ecoli crystal structure.) I'm seeing the same split, two pieces with the same function whose summed size "equals" an intact DnaE-like DNA polymerse III (alpha), in non-draft (and by phamerator the draft) genomes of several other small clusters: R, AC, CB, DG, and 2-3 singletons. Not all of the pieces are the same size, and in some cases there is a small, intervening "NKF" gene. The big question is: do I continue the trend and call both functions "DnaE-like DNA polymerse III (alpha)", and if not what is the alternative?

Link to this post | posted 27 Nov, 2018 01:06
jawsWPI	Is the web site down? A student and I tried opening the site this afternoon–nothing happened. I tried just now (8 pm Monday) and keep getting "502 Bad Gateway". Thanks. JoAnn

Link to this post | posted 22 Feb, 2018 16:26

jawsWPI

Found the issue and solution; still do not know what caused it to happen in the first place. For some reason DNA master thought there were regions in genes when there were none. It wasn't obvious–when you clicked regions for the affected genes it looked exactly like unaffected genes: a single set of blank boxes for the start, stop and length. However you could click "delete" region in the affected genes and get the correct dialog: i.e. a warning box asking if you wanted to really delete this region, which required a response (yes in my case). I found and deleted all false regions and the validate warning is gone. SEA experts–any idea why "hidden" single regions might have happened in the first place?

Link to this post | posted 21 Feb, 2018 19:46

jawsWPI

My students are seeing a very weird validation result. It wasn't present in the original merged file which showed fixable or expected messages, but appeared later after students started editing the merged files (attachment). I have tried everything I could think of to get rid of this: re-numbered, re-tagged, recreate documentation, saved and reopen (separately in sequence) and still have the weird "join(0. .0) Region lengths not correct complement (join(0. .0)) Region lengths not correct" messages. Has anyone else seen this? Is it an issue for final QC? Is there a solution out there? 97Kb