I think you are asking if the virus sequence changes over time, and so the alignment of virus sequence against other virus sequence changes over time? Yes, the virus sequence can change and evolve over time. That is why there are so many different sequences for influenza virus depending on the year ...

How are things going with your research Ryan. I wsan't sure if there were some questions we needed to sort out?
-Caroline

Science buddies has a nice page about all the different types of agar https://www.sciencebuddies.org/science-fair-projects/project_ideas/MicroBio_Agar.shtml Kamran is right that growing agar plates that outside of a lab (and even in some lab environments) it can be difficult to avoid contamination. ...

Thanks for the extra info. It enables me to go and try doing what you are doing and see why it might not get the expected result. I searched A/New Caledonia/20/99 AND 566[SLEN] and as you found nothing comes up. This is a very specific search for the full length hemagglutinin. Maybe no one has publi...

Hi, In order to help you trouble shoot we need some more details about what exactly you did. Which strains of flu are you trying to retrieve? Maybe you had a typo in the name of the strain you chose? What happens if you try the test example "A/Wisconsin/67/2005 AND 566[SLEN]" does that wor...

Ryan,
I checked with Amy but they can't get back to us right away. Since you need it so quick, please go to the team page for the database that I work for and you can see the public information.
http://www.pharmgkb.org/home/pharmgkb_team.jsp
-Caroline F. Thorn, Ph.D.

\i'm happy to be listed as a mentor but I'll get Amy from Science buddies to sort this out. There are rules about what can be posted on these boards and contact between students and experts.
best of luck,
\caroline

Hi Ryan, Hope you are having a good winter vacation. \\\\\\\\\\\\\\\\\\you have doen a good job with putting together your abstract.i just have a couple of suggestions: \first with the title. i would suggest you say up front that you are using a bioinformatics approach. \maybe bioinformatic comparis...

Hi Ryan, I am just on my way to catch a flight to england so can't answer everything now. I will try and post later in the week. I am happy to look at your abstract for college applications - when is it due? and where are you applying? (you might want to style it a little differently depending on wh...

Hi Ryan, Sorry its been a while. 1. Can you import the jpg as a picture into a word file or powerpoint and attach that? otherwise i will ask Amy the board administrator. 2. That does look like another useful website but we have got some wires crossed with the numbering here- the numbering you have f...

Hi Ryan, 1. Let's recap on some terminology. There are different parts to a gene - these include the parts that make the protein and the parts that control when the protein is made. The whole sequence of the gene on the chromosome is called the genomic sequence. When the gene undergoes transcription...

Hi Ryan, Good job with getting your target area outlined. I think at this stage I would choose the largest target area to be the putative motif so from your numbers below that would be 2899-3267. The Gbrowse section you found at zfin is for looking at how zfin genes are arranged on the chromosomes. ...

Hi Ryan, Good job. 3000-6500 is a bit too broad a range to be a motif. I would expect a motif to be approx 100bp or less. Or did you mean there is a cluster near 3000 and one near 6500 and both might be candidate motifs? If you are going to use those regions to test for function then you would need ...

Hi Ryan, Good job with getting all your alignments for anxa5! I'm having trouble with all the graph styles too - attached is quick sketch of what i am looking for. Human genes on the y axis and bases numbering for anxa5 on the x axis. A line for each human gene that shows the span from start to stop...

Hi Ryan, The numbers get moved with the formatting too. It can be hard to get them to line up again. Either note the results as you get them or if its too late for that measure from the start of the sequence shown. The number at the beginning is the first base shown so you can highlight the bases up...

When you pasted these into the word file it changed the formatting a little so the colons that indicate identity between the sequences shifted and the numbers don't line up as well. There is a trick that will help with this. Change the font formatting to one where the letters are all the same width ...

i think you did the right thing choosing the sequence, it shouldn't matter but better to be consistent if possible.

Yes, include all the regions of similarity from each gene.

Looking good,
Caroline

Hi Ryan, I have tried to do a mock up of what i was thinking. See attached word file. It is comparisons for some made up genes. Then see how i logged them in the excel - but i couldn't upload both files so just pasted the table into the word file. Hope this gives good illustration of what i meant. I...

We need to figure out a way to test if the regions highlighted as similar/identical in your comparisons are the same regions that keep coming up or all different. Here is a possible way : make a spreadsheet that gives the range of bases in the gene. Are you good with Excel? Pick one zebrafish gene a...

Thanks for your answers Ryan. It's good to know what you are aiming for and that you don't have any pressing deadlines. It's great that you are doing this from our own initiative and interest. One key thing I forgot to ask was what grade are you in? About the zebrafish list: i went back and looked a...

Hi Ryan, I am happy to help. I juggle working as a curator with being a mom and so can't be a full time mentor for you but try and get to your questions! This is a really good project and I want to make sure I am setting you off on the right path at the beginning that why so much talk on the best ap...

Hi Ryan, Sorry its taken so long. I've been busy with work and then needed to really think about your project before answering. I think we need to work at refining your hypothesis and that should make it easier to narrow down what you have to do. You don't have a clear hypothesis right now. Thats ok...

Hi Ryan, Some answers... >1)I think there is no difference in sequence between them. Is it ok to use either one to compare? I think so but try and be consistent and keep a record. >2)And when you compare it is good to use all sequences even though it is really long. Right? Yes, use the whole gene. >...

Hi Ryan, You are welcome, I am happy to help a student who is enthusiastic and looking to learn. Yes, I think using the whole gene sequence is the best idea -it just happens that PSRC1 is pretty short. Some of the other genes will be much longer but the alignment should still work. Since you are not...

i'm having trouble getting the screenshots to upload as the file is too big. i'll ask the science buddies people for help and see if they can do it. sorry i am not better at explaining in words!
-Caroline

Hi Ryan, Maybe I wasn't clear enough with my instructions for retrieving the sequence for PSRC1. It should only be a small part of Genome Reference Consortium Human Build 37 (GRCh37), Primary_Assembly that corresponds to the PSRC1 gene - about 3279bases long. Yes the whole Genome Reference Consortiu...

Hi Ryan, I did a test using genomic sequence of PSRC1 (human) and ANXA5 (zebrafish), at the ALIGN Query website that was the first link on the list of all the sequence comparison (http://xylian.igh.cnrs.fr/bin/align-guess.cgi). I too got error messages and it said my email was wrong or something. So...

Hi Ryan,

ALIGN should work for long sequences so i'll have a go myself to check and let you know.

-Caroline

Hi Ryan, I would try and pick all the reference sequences for your human genes from the same source if possible. So choose the "Genome Reference Consortium Human Build 37 (GRCh37), Primary_Assembly" where possible - if there isn't one from this source then make a note of it and which alter...

Hi Ryan, So I have read through the project idea website and the goal of that project is a little different from yours so we need to alter the protocol a little. The sample project is looking at points of variation found in the same gene but different people, SNPs. What i think you wanted to do was ...