I think there is a problem in my understanding on the numbering used for base pairs in a chromosome. Can you please clarify my query? In short, the query is "Whether the negative strand of a chromosome is numbered in ascending order just like the positive strand, or in the descending order?"
To be descriptive, the bases in the positive strand is numbered as [1-2-3-...-maximum_chromosome_length]. Is the complementary negative strand also numbered in databases like this or as [maximum_chromosome_length- ... -3-2-1]? I have retrieved a sequence from the base 1 to 100 in positive strand of chr 1 and also the same from negative strand and I have seen that they are completely different. Because either the numbering is: + strand: 1 2 3 ... x - strand: 1 2 3 ... x or is: + strand: 1 2 3 ... x - strand: x ... 3 2 1 Which one is correct? what are you using? > Hi Tapas, > > My apologies - the browser is looking for default values to enter into > the position text box. The link below should work for hg18, > chr6:1000-1500: > > http://genome.ucsc.edu/cgi-bin/hgc?g=getDna&i=mixed&c=chr6&l=999&r=1500&db=hg18 > > Best, > Mary > --------------------- > Mary Goldman > UCSC Bioinformatics Group > > On 6/24/10 4:57 PM, Tapas Bhadra wrote: >> Sir, >> Thanks for your reply. But when I am trying to go into the site it >> shows that "hashMustFindVal: 'c' not found " in that page. >> >> Pleaes reply at your earliest convenience. >> >> Thanking you, >> Tapas Bhadra, >> Senior Research Fellow, >> Indian Statistical Institute, >> Kolkata, >> India >> >> >> >>> Hi Tapas, >>> >>> Whether you obtain the DNA sequence through our downloads page or the >>> "DNA" button in the blue bar when you are viewing an assembly, it >>> always >>> defaults to the positive strand. The easiest way to get DNA for a short >>> sequence, such as the one you mentioned in your email, is to use the >>> "get DNA" feature (http://genome.ucsc.edu/cgi-bin/hgc?g=getDna). Simply >>> type in the coordinates and click the "get DNA" button. Note that you >>> can also get DNA from the negative strand by clicking the "reverse >>> complement" check box. >>> >>> I hope this answers this question and both of your questions that were >>> emailed to our team yesterday. Please feel free to contact the mail >>> list >>> again if you require further assistance. >>> >>> Best, >>> Mary >>> ------------------ >>> Mary Goldman >>> UCSC Bioinformatics Group >>> >>> On 6/24/10 4:33 AM, Tapas Bhadra wrote: >>> >>>> Dear Sir, >>>> I am a research fellow at the Indian Statistical Institute, >>>> Kolkata, >>>> India. >>>> >>>> I have downloaded the sequences of all the chromosomes. Can you please >>>> inform me that if I need sequences from 1000bp to 1500bp of chr 6 from >>>> +ve >>>> strand and also from 1000bp to 1500bp of chr 6 from -ve strand, then >>>> how >>>> will I obtain those information. Will they be same? >>>> >>>> Is your database strand specific? If yes then which strand it >>>> annotates >>>> for the sequence and for this strand specific database how will we >>>> obtain >>>> sequential information from the reverse strand? >>>> >>>> Pleaes reply at your earliest convenience. >>>> >>>> Thanking you, >>>> Tapas Bhadra, >>>> Senior Research Fellow, >>>> Indian Statistical Institute, >>>> Kolkata, >>>> India >>>> This mail is scanned by Ironport >>>> >>>> >>>> _______________________________________________ >>>> Genome maillist - [email protected] >>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>>> >>>> >>> This mail is scanned by Ironport >>> >>> >>> >> This mail is scanned by Ironport >> >> > This mail is scanned by Ironport > > This mail is scanned by Ironport _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
