SEA-PHAGES | Starterter Analysis of our nearly finished sequence

Link to this post \| posted 03 Mar, 2016 22:52
GregFrederick@letu.edu	We are almost finished with our annotation of our first two genomes. We have added multiple genes that DNA Master did not call originally. QUESTION: Is there a way to manually input our near completed sequence into Starterator to see what it thinks about the start codons we have chosen? If so, how? If not, this would be a really nice feature to add. (I'm guessing the feature is already available. So please tell me how.) Thanks.

Link to this post | posted 03 Mar, 2016 22:52

We are almost finished with our annotation of our first two genomes. We have added multiple genes that DNA Master did not call originally.

QUESTION: Is there a way to manually input our near completed sequence into Starterator to see what it thinks about the start codons we have chosen?

If so, how?

If not, this would be a really nice feature to add.

(I'm guessing the feature is already available. So please tell me how.)

Thanks.

Link to this post \| posted 04 Mar, 2016 17:24
cdshaffer	Starterator does have the "One unphamerated gene" routine which you select from the menu that always starts with "Whole phamerated phage". Starterator asks for the name of the phage, the full fasta sequence file, and info on the gene (coordinates and strand) you would like to analyze. I have only looked at the code for that routine briefly but it is clear that starterator is extracting the region of interest, doing some calculations to guess the pham it would be in, and then running the starterator analysis. Unfortunately, my students and I have only had limited success with that particular routine. I gave up using it in class. It appears to work on some phage/genes but not others. So you can certainly try it and if you get a report, great. If not, the only solution I know of would for either you or someone you know to create an updated phamerator database with your improved annotations so you can do a whole gene report in starterator. Phamerator database creation is typically done with unix, python and sql command line but Randal DeJong just published a web based system for phamerator database management called phamDB. Once you get it set up (still not trivial but certainly easier than command line phamerator) you can easily remove/add/update phage in your database. Here is the link to the bioinformatics paper. Oh, and by the way, Congratulations Randal! He presented preliminary work on this at the last symposium and its nice to see it has now been published. Edited 04 Mar, 2016 17:26

Link to this post | posted 04 Mar, 2016 17:24

cdshaffer

Starterator does have the "One unphamerated gene" routine which you select from the menu that always starts with "Whole phamerated phage". Starterator asks for the name of the phage, the full fasta sequence file, and info on the gene (coordinates and strand) you would like to analyze. I have only looked at the code for that routine briefly but it is clear that starterator is extracting the region of interest, doing some calculations to guess the pham it would be in, and then running the starterator analysis.

Unfortunately, my students and I have only had limited success with that particular routine. I gave up using it in class. It appears to work on some phage/genes but not others. So you can certainly try it and if you get a report, great. If not, the only solution I know of would for either you or someone you know to create an updated phamerator database with your improved annotations so you can do a whole gene report in starterator.

Phamerator database creation is typically done with unix, python and sql command line but Randal DeJong just published a web based system for phamerator database management called phamDB. Once you get it set up (still not trivial but certainly easier than command line phamerator) you can easily remove/add/update phage in your database. Here is the link to the bioinformatics paper. Oh, and by the way, Congratulations Randal! He presented preliminary work on this at the last symposium and its nice to see it has now been published.

Edited 04 Mar, 2016 17:26

Link to this post \| posted 04 Mar, 2016 17:48
GregFrederick@letu.edu	Thank you for all that info! GF

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Starterter Analysis of our nearly finished sequence