Hi Otis
Sorry I've been so brain dead lately. It comes and goes and when it's bad it's very bad. Just got up from about a 3 day nap (grins) I currently have 3 working brain cells and thought I'd try to use them.
The whole BLAST thing sounds really cool. I'm guessing here that what is needed to do BLAST is the gene sequences so that you can run two against each other?????
http://www.ncbi.nlm.nih.gov/genomes/GenomesHome.cgi?taxid=10239
Looks like a primer on the BLAST
http://www.ncbi.nlm.nih.gov/sites/entrez?db=nucleotide
This looks like where to get the nucleotide sequences like the ones from the Alter Paper
When I typed in XMRV I got 638 hit's some with patents????? and the complete genomes of VP 62/42/35 (these are at the very end of the 638 listed)
http://www.ncbi.nlm.nih.gov/nuccore/EF185282.1
This link is the entire nucleotide sequence, I think you can use the Accession number in the BLAST????? and it loads the sequence?????
On the Friend Murine Leukemia virus there is a whole genome on the FB29 it's link is here
http://www.ncbi.nlm.nih.gov/nuccore/Z11128.1 there does seem to be a lot of variants of this virus, A LOT of variants.
The Moloney MLV (which is classed as a PMLV) is here
http://www.ncbi.nlm.nih.gov/nuccore/J02255.1
Now what I can't figure out is how to find out if a MLV sequence comes from a particular mouse strain. Like what Vince was talking about with the, and here's another fuzzy, either an MLV sequence from Alter/Lo paper was a match for the 129 mouse strain or XMRV is a match for the 129 mouse strain. But where does one find MLV's listed with reference to specific lab mice???? (head scratch)
I did find this information on the Jackson Laboratories site
http://jaxmice.jax.org/strain/004178.html about the 129 strain. (if you click on the tabs it get's into some facinating reading if you have time to read through it, grins) and that lead to this page
http://jaxmice.jax.org/protocolsdb/...P2_MASTER_PROTOCOL_ID,P2_JRS_CODE:5200,004178 which list's phenotyping, primers and other information for laboratory use but I still don't know how to match it all up and come to a reasonable piece of information that we can use. ?????
You probably have all the above information and are happily BLASTING away. (grins) but just in case I could add anything I though I toss this stuff out there. Who knows maybe the links will come in handy down the road. (big grins)
George,
I'm not entirely sure how one patents a sequence but I'm only going to consent to a study if any and all patents for the little buggers messing me up are ALL MINE.
You ran across some good stuff. I had found VP62, which is very (99+%) similar to the 2 complete Lombardi sequences I found. FYI - you can further qualify a search by entering 'XMRV Lombardi' and you get all the XMRV sequences associated with the 1960's Green Packers - or the Science study. Whoever drew more blood. :Retro smile: Since there are six sequences it must be the Science Study.
The genomes list was very interesting and merits more poking around.
Basically you can compare known sequences against each other, or against the genome DBs, the mouse on being of interest here. I have a lot to learn about all the options, graphical views, etc. - although it's easy to create a phytogenetic tree given a list of sequences.
For anyone who wants to play with this here's easy example for any fellow geeks out there:
- If you follow
this link
- Then paste GQ483509.1 in the box below the text "Enter accession number, gi, or FASTA sequence"
- Make sure the check box next to "Align two or more sequences" is checked
- Then paste GQ483508.1 in the (second) box below the text "Enter accession number, gi, or FASTA sequence"
- Then go to the bottom of the page and click the big 'BLAST' button
If my example was any good you've just compared two partial sequences from the Science paper.
At the bottom is the interesting part, the results depicting the 'alignment'. It looks (something) like the following:
>gb|GQ483509.1| Xenotropic MuLV-related virus isolate WPI-1138 putative polyprotein
gene, partial cds
Length=366
Score = 652 bits (353), Expect = 0.0
Identities = 359/362 (99%), Gaps = 0/362 (0%)
Strand=Plus/Plus
Query 1 TTGCAGCACTGGGGAGATGTCCAGCGCATTGCATCCAACCAGTCTGTGGATGTCAAGAAG 60
Sbjct 1 TTGCAGCACTGGGGAGATGTCCAGCGCATTGCATCCAACCAGTCTGTGGATGTCAAGAAG 60
Query 61 AGGCGCTGGGTTACCTTCTGTTCCGCCGAATGGCCAACTTTCAATGTAGGATGGCCTCAG 120
Sbjct 61 AGGCGCTGGGTTACCTTCTGTTCCGCCGAATGGCCAACTTTCAATGTAGGATGGCCTCAG 120
Query 121 GATGGTACTTTTAATTTAGGTGTTATCTCTCAGGTCAAGTCTAGAGTGTTTTGTCCTGGT 180
Sbjct 121 GATGGTACTTTTAATTTAGGTGTTATCTCTCAGGTCAAGTCTAGAGTGTTTTGTCCTGGT 180
Query 181 CCCCACGGACACCCGGATCAGGTCCCATATATCGTCACCTGGGAGGCACTTGCCTATGAC 240
Sbjct 181 CCCCACGGACACCCGGATCAGGTCCCATATATCGTCACCTGGGAGGCACTTGCCTATGAC 240
Query 241 CCCCCTCCGTGGGTCAAACCGTTTGTCTCTCCTAAACCCCCTCCTTTACCGACAGCTCCC 300
Sbjct 241 CCCCCTCCGTGGGTCAAACCGTTTGTCTCTCCTAAACCCCCTCCTTTACCGACAGCTCCC 300
Query 301 GTCCTCCCGCCCGGTCCTTCTGCGCAACCTCCGTCCCGATCTGCCCAATACACTGCCCTT 360
Sbjct 301 GTCCTCCCGCCCGGTCCTTCTGCGCAACCTCCGTCCCGATCTGCCCTTTACCCTGCCCTT 360
Query 361 AC 362
Sbjct 361 AC 362
A few notes. There are vertical bars between the top (subject) and bottom (Query) rows, but the spacing came out all wrong even using courier font.
For places where a pair isn't the same there is no vertical bar. There are three such cases in this example, near the bottom.
I bolded a couple of things.
- Identities are the number of total matches over the total in the comparison.
- Gaps are places where there is a gap (or insertion) in the compared sequences. For these two there are no gaps.
Here are the two complete Lombardi sequences IDs which will prove to be a more interesting example.
GQ497344.1
GQ497343.1
Happy blasting.
Otis