SEA-PHAGES | All posts created by jawsWPI

Link to this post \| posted 18 Jun, 2020 14:57
jawsWPI	I would agree that the two smaller ones should be NKF but, the 1200bp is probably a minor tail. An HHPred run analysis of the 1200bp protein should give good hits to collagen-like or glycine-rich proteins if it is a minor tail. The gene count in your A3 may be off because gene 1 (HNH endonuclease) is often not included in the auto-annotation and has to be added manually.

Posted in: Cluster A Annotation Tips → minor tail proteins

Link to this post \| posted 02 Jun, 2020 16:49
jawsWPI	QCing Chivey, and it looks like we are perpetuating another bad minor tail protein call in the EF phages. Pham 38688, found in several different clusters, is a small protein (350 -400 bp) well upstream of the tapemeasure protein in EF (around gp22); a significant majority of the pham members assign NKF. Best HHPred hit (see attached) in all non-draft EF is from pfam (phage HK97-gp10) 'putative tail-component' (TIGRFAMs calls this same gene a model for an uncharacterized, highly divergent bacteriophage family); no good PDB or collagen or coiled-coiled domains. Based on this and the May 27 SMART conversation I'm changing Chivey's to NKF–heads-up for other EF. 9Kb

Link to this post | posted 02 Jun, 2020 16:49

jawsWPI

QCing Chivey, and it looks like we are perpetuating another bad minor tail protein call in the EF phages. Pham 38688, found in several different clusters, is a small protein (350 -400 bp) well upstream of the tapemeasure protein in EF (around gp22); a significant majority of the pham members assign NKF. Best HHPred hit (see attached) in all non-draft EF is from pfam (phage HK97-gp10) 'putative tail-component' (TIGRFAMs calls this same gene a model for an uncharacterized, highly divergent bacteriophage family); no good PDB or collagen or coiled-coiled domains. Based on this and the May 27 SMART conversation I'm changing Chivey's to NKF–heads-up for other EF.

Posted in: Cluster EF Annotation Tips → Upstream minor tail (pham 38688) really NKF

Link to this post \| posted 05 Feb, 2020 15:40
jawsWPI	Hi Jamie, Are you using the dropdown function choice menu in PECAAN? My students couldn't get a green check mark unless they type in an exact match to the functions in PECAAN, or actually selected an existing function from the dropdown menu. And of choice clicking 'save' BEFORE leaving the page.

Posted in: PECAAN → PECAAN Down?

Link to this post \| posted 28 Jan, 2020 17:30
jawsWPI	How long does it take PECAAN to update pham numbers for the Starterator and phageDB links? We are annotating on PECAAN, and over the past 2 days have run into several instances where these links gave the following error message: "Page/Report not found Error 404" for a gene that isn't an orpham. The stand-alone phamerator map pham numbers are accurate (embedded PECAAN pham map numbers are not), and can be used on phagesDB or the stand-along starterator site to get information. So, it looks like this is a PECAAN update issue.

Link to this post | posted 28 Jan, 2020 17:30

jawsWPI

How long does it take PECAAN to update pham numbers for the Starterator and phageDB links?
We are annotating on PECAAN, and over the past 2 days have run into several instances where these links gave the following error message: "Page/Report not found Error 404" for a gene that isn't an orpham. The stand-alone phamerator map pham numbers are accurate (embedded PECAAN pham map numbers are not), and can be used on phagesDB or the stand-along starterator site to get information. So, it looks like this is a PECAAN update issue.

Posted in: PECAAN → PECAAN Down?

Link to this post \| posted 06 Jun, 2019 12:51
jawsWPI	How hard and fast is the minor tail protein size range (1-3kb)? I'm reviewing an A1 annotation that has assigned the 'minor tail protein' function to 333bp, 348 bp and 447 bp ORF's, mostly based (I think) on a FEW cases in each pham that have given this functional assignment to similarly (small) sized ORFs. I want to change these all to NKF, first based on size and second based on total number of minor tails of the correct size and position.

Link to this post | posted 06 Jun, 2019 12:51

jawsWPI

How hard and fast is the minor tail protein size range (1-3kb)?
I'm reviewing an A1 annotation that has assigned the 'minor tail protein' function to 333bp, 348 bp and 447 bp ORF's, mostly based (I think) on a FEW cases in each pham that have given this functional assignment to similarly (small) sized ORFs. I want to change these all to NKF, first based on size and second based on total number of minor tails of the correct size and position.

Posted in: Cluster A Annotation Tips → minor tail proteins

Link to this post \| posted 10 Apr, 2019 19:05
jawsWPI	Thanks Chris. That worked and I could see the changes during each iteration.

Posted in: PECAAN → New Features in PECAAN

Link to this post \| posted 10 Apr, 2019 15:27
jawsWPI	Lee Hughes My best guess is that the field isn't actually empty, but has something in it (a space perhaps, or a hard return), which is why it isn't being labeled. You probably need to make sure those fields are actually empty in order to get them to write. If you are copying and pasting into the Function field at some point in the process, you might have an extra hard return in the data (this can happen when copying from other programs) that is still in the field and causing the problem. Lee This was also my thought and I have done everything I can think of to make sure the fields are truly empty before using the DNA master tools to transfer copy data from one field to another. The hidden space or hard return appears to be imbedded in the PECAAN text file that I'm copying into DNA master documentation before parsing. Here is the only hint I have: the last gene product, which is NKF, actually is labeled as hypothetical. I've looked at the text file (copied below) and the only difference is that there isn't a "CDS" immediately after the double quotes (signifying the start of the next feature call) for this last gene. Attached is what the text file looks like in notepad, but below is what I got when I copied the highlighted section and pasted that text into this message. There definitely seems to be a carriage return right after every note except the last one. CDS 54801 - 55664 /gene="81" /product="gp81" /locus tag="NarutoRun_81" /note="" CDS 55666 - 56145 /gene="82" /product="gp82" /locus tag="NarutoRun_82" /note="" Claire is this something new that we have to work around (this is the first time I have used PECANN for the full annotations)? I assume there haven't been issues before when parsing PECAAN CDS functions text files. 5Kb

Link to this post | posted 10 Apr, 2019 15:27

jawsWPI

Lee Hughes
My best guess is that the field isn't actually empty, but has something in it (a space perhaps, or a hard return), which is why it isn't being labeled. You probably need to make sure those fields are actually empty in order to get them to write. If you are copying and pasting into the Function field at some point in the process, you might have an extra hard return in the data (this can happen when copying from other programs) that is still in the field and causing the problem.

Lee

This was also my thought and I have done everything I can think of to make sure the fields are truly empty before using the DNA master tools to transfer copy data from one field to another. The hidden space or hard return appears to be imbedded in the PECAAN text file that I'm copying into DNA master documentation before parsing. Here is the only hint I have: the last gene product, which is NKF, actually is labeled as hypothetical. I've looked at the text file (copied below) and the only difference is that there isn't a "CDS" immediately after the double quotes (signifying the start of the next feature call) for this last gene.
Attached is what the text file looks like in notepad, but below is what I got when I copied the highlighted section and pasted that text into this message. There definitely seems to be a carriage return right after every note except the last one.

CDS 54801 - 55664
/gene="81"
/product="gp81"
/locus tag="NarutoRun_81"
/note=""

CDS 55666 - 56145
/gene="82"
/product="gp82"
/locus tag="NarutoRun_82"
/note=""

Claire is this something new that we have to work around (this is the first time I have used PECANN for the full annotations)? I assume there haven't been issues before when parsing PECAAN CDS functions text files.

Posted in: PECAAN → New Features in PECAAN

Link to this post \| posted 09 Apr, 2019 19:22
jawsWPI	Claire Rinehart Tammy, We currently do not place the function into the function box in our DNA Master Full Annotation export. Welkin just pointed out to me that the online guide tells how to generate minimal files from the complete notes when functions are recorded in the function field. We will work on adding this feature to the complete file export. Meanwhile, you can use the Export CDS Function button on the export page of PECAAN to export a file that can be copy/pasted into the DNA Master Documentation page which will parse the functions into the notes field. These minimal functions can then be copied en masse into the product or function fields in DNA Master by clicking on the right hand triangle in the Notes field. Thanks, Claire I'm trying to generate a DNA master minimal file using copy/paste/parse from an exported CDS function, but it won't auto-label the blank products as "hypothetical" it's just leaving them blank. I tried using the 'new SEA format' full annotation, but that puts NKF in the function field which also causes the same problem if you follow the entire step sequence for generating a minimal file from the guide (from the guide: "NKF" is also not considered default, and won't be overwritten". Is anyone else having this problem? Is there a solution besides pasting in "hypothetical" in to all the blank product fields?

Link to this post | posted 09 Apr, 2019 19:22

jawsWPI

Claire Rinehart
Tammy,
We currently do not place the function into the function box in our DNA Master Full Annotation export. Welkin just pointed out to me that the online guide tells how to generate minimal files from the complete notes when functions are recorded in the function field. We will work on adding this feature to the complete file export. Meanwhile, you can use the Export CDS Function button on the export page of PECAAN to export a file that can be copy/pasted into the DNA Master Documentation page which will parse the functions into the notes field. These minimal functions can then be copied en masse into the product or function fields in DNA Master by clicking on the right hand triangle in the Notes field.
Thanks,
Claire

I'm trying to generate a DNA master minimal file using copy/paste/parse from an exported CDS function, but it won't auto-label the blank products as "hypothetical" it's just leaving them blank. I tried using the 'new SEA format' full annotation, but that puts NKF in the function field which also causes the same problem if you follow the entire step sequence for generating a minimal file from the guide (from the guide: "NKF" is also not considered default, and won't be overwritten" smile

.

Is anyone else having this problem? Is there a solution besides pasting in "hypothetical" in to all the blank product fields?

Posted in: PECAAN → New Features in PECAAN

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!

Posted in: Functional Annotation → Membrane protein

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 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

Posted in: Functional Annotation → Membrane protein

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