Link to this post | posted 17 Jan, 2017 21:31

Tamarah_Adair

Today we tried to import our FASTA files and autoannotate. The majority of the students were able to accomplish this, although it took longer than usual. Several students and myself were never able to get the file to load. As I tried to recreate the problem with Jason K (our IT person) we have been hung up on the EXPORT. The Features table never fills. We are working with the most recent update 12.3 We want to know 1. during this process is there interaction with servers (genemark? glimmer?) on the network or is this all local at this point? 2. If there is network interaction is there a way to generate a log or a trace file so we can see what is going on? Thanks! Tammy

Link to this post | posted 29 Aug, 2016 18:15
Tamarah_Adair	Does anyone have experience mining metagenomic data for phage sequences? I have a colleague that studies the microbiome of stool samples. I am wondering how to find phage in the microbiome.

Link to this post | posted 24 May, 2016 19:01
Tamarah_Adair	I am so sad to hear of this tragic accident. David was always willing to share and talk about science and I admired his enthusiasm and dedication to his students. Blessings and prayers for God's peace and comfort to all his friends and family.

Link to this post | posted 15 Feb, 2016 20:48

Tamarah_Adair

Is anyone else having a problem with auto annotation today? It acts like it is working, but then gives a Glimmer failure and nothing is saved to Features. Auto-annotation of Extracted from FastA Library KylieMac.fasta9 begun at 2:46:10 PM Predicting genes at 2:46:10 PM Predicting tRNAs at 2:46:18 PM Parsing genes at 2:46:19 PM Learning genes at 2:46:19 PM Skipping BLAST at 2:46:19 PM Doing Profile at 2:46:19 PM Performing Frames Analysis at 2:46:19 PM Skipping Start Codon Analysis at 2:46:19 PM Performing Gray Holes Analysis at 2:46:20 PM Creating GC-Content Plot at 2:46:20 PM Auto-annotation Complete at 2:46:25 PM Profile for genome Extracted from FastA Library KylieMac.fasta9 Index,Name,Direction,Strand,Feature_Start,Feature_Stop,Feature_Length,Feature_Type,

Link to this post | posted 05 Feb, 2016 18:30
Tamarah_Adair	Can someone please tell me how to share from the virtual box/phamerator files to the Mac desk top?

Link to this post | posted 04 Feb, 2016 21:06
Tamarah_Adair	I just did a BLAST all genes on KylieMac and received the results in 15 minutes- in the Features BLAST window! Oh Happy Day!

Link to this post | posted 04 Feb, 2016 19:40
Tamarah_Adair	Yesterday we tried this new version out in lab and I was able to BLAST. The newest version to the box account is at the following link: https://baylor.box.com/s/sct7ixend1d29cn5n7qjlbcfod98hyny Changes: Rebuilt wine bottler package based on wine bottler 1.8rc4 (needed for El Capitan support) Updated to current version of DNAMaster (5.22.23 dated 1/26/16) Edited 04 Feb, 2016 20:06

Link to this post | posted 01 Feb, 2016 23:02
Tamarah_Adair	We can not get Starterator to connect to the database. We changed the server and database to match the Actino_Draft in phamerator, but we still get an error with any gene from any genome.

Link to this post | posted 01 Feb, 2016 22:49

Tamarah_Adair

Today I received a few inquiries about using the DNAMaster in WINE. The link that is posted should still work. This is the comment I have from our IT- Users can download the box version and run it and it will update itself as usual. Once the updates have ran, that user will have the equivalent of what is in G42. We are using this version- but we are not able to BLAST from DNAMAster. I am getting a directory (?) error after a few minutes that says OLE error. Does anyone have any ideas on how to fix this? We can use the NCBI and phagesdb sites for annotation, but eventually we are going to need to have BLAST results in DNAMaster. Theoretically, this version is detecting DNAMaster updates, but I am wondering if there is a new link out to NCBI that it is not seeing? We are running DNA Master within the WINE configuration. The installer has been copied and you should be able to get to it from this link. https://baylor.box.com/s/295to06pr1cpztqiu2jn0h77iy3vkanz THANKS!

Link to this post | posted 22 Jan, 2016 20:17
Tamarah_Adair	Is there a consensus on how Arthrobacter annotations should be recorded? I am wondering about GeneMark and BLAST. Are we using GeneMArkS or A. aurescens? and NCBI BLAST or phagesdb BLAST? or both?