Friday 9 September 2011

I am not a Bioinformatician: 1. Experiences with UCSC DAS

I am not a Bioinformatician but I often want to do things Bioinformaticians say are easy. This is the first in a possible series of blogs about my experiences with Bioinformatics, text mining, etc. I'd be very happy to receive comments on the approaches I try or hints on how to do what I am trying to do more easily. For now I am not learning to program or run scripts from a command line. I am happy to try something in Galaxy.
Part of the reason for these posts is so I can remeber how to do this next time myself.
This is meant to be the non-Bioinformaticians way of doing things!

I used to just send an email to one of the Bioinformaticians at work but I couldn't help but take the hint that they had work to do as well. So now I'll usually try to find out if I can do what I want myself with publically available, usually web-based tools. I figure that even if I don't succeed my trying is evidence I'm not just abusing their better experience. It also helps me better explain what I want so they don't do some work for me and then I say how nice it is but it is not really what I thought I wanted after all.  


UCSC Distributed Annotation Service (DAS):
 The "DAS" server allows you to download data directly from UCSC. I suspect it is built to be queried from under the hood rather than through a URL. However it is an easy way to get the sequence from genomic coordinates so I like it.

There is a simple FAQ here. And a query for a sequnce looks like this http://genome.ucsc.edu/cgi-bin/das/hg18/dna?segment=chr2:51409549,51409749 which will return 200bp of sequence from chr2 in Hg19 build of the Human genome.

Here's how I used DAS and other tools to design some primers from a SNP:

Designing PCR primers from an dbSNP rsID: I am hoping to design some PCR assays to look at regions around SNPs. I got a list of SNPs from a colleague wth lots of information about them position, alleles, MAF, etc. However I wanted to take this list and design PCR primers to all 24 SNPs as quickly as possible. 
Getting SNP locations: I was already sent the locations along with rsID's but I wanted to see if I could find them myself. I like UCSC and it is usually my first port of call when looking for sequence information. In this case I simply entered an rsID into the UCSC position/search box (Image:UCSC RsID search) and then clicked through the link (Image: UCSC rsID results). This gives me the all important location information, chr1:4181020-4181020 in the case of rs10799216. 
Getting flanking sequence: I  used Excel (not a bioinformaticians favourite tool) to create a UCSC DAS address (Image: Excel to create DAS address) to pull out the flanking regions 100bp either side of the SNP (Image: UCSC DAS results). 
Designing suitable primers: I used the sequence results from the DAS query in Primer3 (image: Primer3 Input) wth the parameters Targets=100,2 (primers surronding the 2 bases at position 100), ProdcutSizeRange=30-75 (I want short products) and NumberToReturn=50 (50 sets of primers). Hey presto PCR primers (Image: Primer3 Output)

Now I can get on and order some primers to test in the lab, where I feel much more in my conmfort zone.




UCSC rsID search



















UCSC rsID results



















Excel to create DAS address

















UCSC DAS results



















Primer3 Input



















Primer3 Output



















SNAP from the Broad


















SNAP query



















SNAP results
 













about the snp data and using excel and word to generate a DAS list and get data fast even though I'm not a bioinformaticiain!!!

3 comments:

  1. WHEN ALL HOPES IS LOST MEDICALLY TO THE CURE OF MY HERPES THE ONLY AWAITING SOLUTION I NEVER KNEW IS DR OGUDU SPELL TEMPLE. FOR THOSE WHO ARE STILL SHARING MY PREVIOUS HOPE IN MEDICAL CURE AS A SOLUTION TO YOUR CURE SHOULD STOP SEARCHING AND GO TO DR.OGUDU FOR INSTANT CURE. CONTACT HIM NOW WITH THE FOLLOWING DETAILS EMAIL ADDRESS [OGUDUSPELLTEMPLE@YAHOO.COM] WHATSAAPP NUMBER +2348106058254 Website---http://oguduspelltemple.wixsite.com/drogudu


    Am COREY ANN from URUGUAY i was suffering from genital herpes, oral herpes, shingles. Before i came in contact with dr.ogudu
    It is no longer news that the Acquired immune deficiency syndrome Herpes Virus is increasing by the day, The fear is that many people living with the sickness are scared of saying it because of the stigma that comes along with it.I am bold enough among many others to state that there is now a potent cure to this sickness but many are unaware of it.I discovered that I was infected with the virus 3 months ago, after a medical check-up. My doctor told me and I was shocked, confused and felt like my world has crumbled. I was dying slowly due to the announcement of my medical practitioner but he assured me that I could leave a normal life if I took my medications, In a bid to look for a lasting solution to my predicament, I sought for solutions from the voodoo world. I went online and searched for every powerful trado-medical practitioner that I could severe, because I heard that the African Voodoo Priests had a cure to the Herpes syndrome. It was after a little time searching the web that I came across one Dr.Ogudu website who offered to help me, He gave me some steps to follow and I meticulously carried out all his instructions. Two days ago to be precise, I went back to the hospital to conduct another test and to my amazement, the results showed that " I am NEGATIVE" You can free yourself of this Herpes virus by consulting this great African Voodoo Priest via this EMAIL [OGUDUSPELLTEMPLE@YAHOO.COM] WHATASPP NUMBER +2348106058254


    WHEN ALL HOPES IS LOST MEDICALLY TO THE CURE OF MY HERPES THE ONLY AWAITING SOLUTION I NEVER KNEW IS DR OGUDU SPELL TEMPLE. FOR THOSE WHO ARE STILL SHARING MY PREVIOUS HOPE IN MEDICAL CURE AS A SOLUTION TO YOUR CURE SHOULD STOP SEARCHING AND GO TO DR.OGUDU FOR INSTANT CURE. CONTACT HIM NOW WITH THE FOLLOWING DETAILS EMAIL ADDRESS [OGUDUSPELLTEMPLE@YAHOO.COM] WHATSAAPP NUMBER +2348106058254 Website---http://oguduspelltemple.wixsite.com/drogudu


    Am COREY ANN from URUGUAY i was suffering from genital herpes, oral herpes, shingles. Before i came in contact with dr.ogudu
    It is no longer news that the Acquired immune deficiency syndrome Herpes Virus is increasing by the day, The fear is that many people living with the sickness are scared of saying it because of the stigma that comes along with it.I am bold enough among many others to state that there is now a potent cure to this sickness but many are unaware of it.I discovered that I was infected with the virus 3 months ago, after a medical check-up. My doctor told me and I was shocked, confused and felt like my world has crumbled. I was dying slowly due to the announcement of my medical practitioner but he assured me that I could leave a normal life if I took my medications, In a bid to look for a lasting solution to my predicament, I sought for solutions from the voodoo world. I went online and searched for every powerful trado-medical practitioner that I could severe, because I heard that the African Voodoo Priests had a cure to the Herpes syndrome. It was after a little time searching the web that I came across one Dr.Ogudu website who offered to help me, He gave me some steps to follow and I meticulously carried out all his instructions. Two days ago to be precise, I went back to the hospital to conduct another test and to my amazement, the results showed that " I am NEGATIVE" You can free yourself of this Herpes virus by consulting this great African Voodoo Priest via this EMAIL [OGUDUSPELLTEMPLE@YAHOO.COM] WHATASPP NUMBER +2348106058254

    ReplyDelete
  2. I feel so blessed again in my marriage after Doctor Oku brought back my husband that separated with me for good 3 mounths. Am Jessica Butler by name from USA. Even though i have mouths all over my body, it won't be enough to thank Doctor Oku for his help upon my life. My husband separated with me for the 3 months and have been in pains and agony without him. So, i searched for help everywhere but nothing worked out not until i meant Doctor Oku who i contacted online. I explained my situation to him and he promised that my husband will get back to me within 24 to 48 hours as far that my heart still beats for him. I believed in him and he prepared a spell for me and my husband called me exactly when Doctor Oku said. He pleaded and said he needs me back and now we are living happily again for the past 9 months. Everyone out there reading my article that needs help should contact him... Email: okutemple@gmail.com or call +2347053113465

    ReplyDelete
  3. I feel so blessed again in my marriage after Doctor Oku brought back my husband that separated with me for good 3 mounths. Am Jessica Butler by name from USA. Even though i have mouths all over my body, it won't be enough to thank Doctor Oku for his help upon my life. My husband separated with me for the 3 months and have been in pains and agony without him. So, i searched for help everywhere but nothing worked out not until i meant Doctor Oku who i contacted online. I explained my situation to him and he promised that my husband will get back to me within 24 to 48 hours as far that my heart still beats for him. I believed in him and he prepared a spell for me and my husband called me exactly when Doctor Oku said. He pleaded and said he needs me back and now we are living happily again for the past 9 months. Everyone out there reading my article that needs help should contact him... Email: okutemple@gmail.com or call +2347053113465

    ReplyDelete

Note: only a member of this blog may post a comment.