Link to this post | posted 08 Nov, 2017 18:15
welkin	Hi Beckie, IT sounds like there is a problem with at least one of the internal tables in the file. If you have the documentation, I would try to regenerate a clean copy of the file by importing the fasta sequence into a new file, pasting in the documentation, and then parsing that. Good luck.

Link to this post | posted 03 Nov, 2017 16:57

welkin

Hi All, Here are the instructions for posting this this forum. First: check the most recent Official Functions list. This list has moved online! Next, if you want to continue with your request: 1. Start a new thread. Don't tack your request onto to the end of an old thread. 2. Present your case by answering the following questions. What is your evidence that your phage protein has the putative new function? Include alignment tool, database used, phage name/gene number, or other evidence. How large are known proteins of this type? Is the size of the protein you are investigating of similar size? Are there conserved residues that are characteristic of this domain? Does your protein have them? Are there normally other conserved domain present in conjunction with this domain? Does your protein have them? 3. please include links to primary literature (preferred!) or database entries that support your claims. 4. Post the amino acid sequence of the gene in question, so we can copy/paste for further analysis if need be. 5. Upload your most current DNA Master file as an attachment to your post. Finally—In general, we don't like to put structural domains down as functional assignments, as too many proteins with a variety of functions can include them. This includes "alpha helix", "beta strand" "coiled coil" "zinc-finger" "von Willebrand factor" etc. Happy functions! Welkin Edited 08 Nov, 2017 15:25

Link to this post | posted 31 Oct, 2017 15:36
welkin	OK, I will add it. Thanks!

Link to this post | posted 31 Oct, 2017 15:36
welkin	YEs! That should be on the list. Thanks for pointing that out.

Link to this post | posted 31 Oct, 2017 15:35
welkin	Isn't that on the list already? OR just needs to be put on there?

Link to this post | posted 31 Oct, 2017 15:32
welkin	Thanks for hunting this down! But no, I don't think we will be putting signal sequences into annotation files.

Link to this post | posted 31 Oct, 2017 15:31
welkin	Hi Jordan, That's great that you found it; but no, we are not including attPs in annotations for GenBank. Best, Welkin

Link to this post | posted 26 Oct, 2017 15:09
welkin	KAtie, This looks like the executable is no longer in the DNA Master folder and it can't find the database files it needs. With the uninstalling/reinstalling did he accidentally drag it out somewhere?

Link to this post | posted 26 Oct, 2017 14:44

welkin

Hi! In order to add a new function to the official list, you need to present more of a case than "I found a domain match". By more of a case I mean: How large are known proteins of this type? Is the size of the protein you are investigating of similar size? Are there conserved residues that are characteristic of this domain? Does your protein have them? Are there normally other conserved domain present in conjunction with this domain? Does your protein have them? In general, we don't like to put structural domains down as functional assignments, as too many proteins with a variety of functions can include them. However, if you are positive that your zinc-finger is DNA binding, then we can consider adding it if you have pursued the rest of the background. Best, Welkin

Link to this post | posted 09 Aug, 2017 15:17
welkin	Hi All, I think we have decided that the best choices for now are: PDB pFam CDD SCOPe 70 The link to the new HHPred website is here, in case anyone has trouble finding it: https://toolkit.tuebingen.mpg.de/#/tools/hhpred However, as of 11am Eastern, on 8.8.2017, the site says it is undergoing maintenance. Hopefully it will be up again shortly! Best, Welkin