Thank you for looking at my question. I am trying to solve this homework question. Consider the problem of sequencing genome by random reads. If G is the length of the entire sequence, L is the length of the read and n is the number of reads, then coverage is defined as nL/G . Now, if we want 50% of the original long sequence to be covered by at least one fragment, how much coverage do we need? I read Lander-Waterman [url]http://www.genetics.wustl.edu/bio5488/lecture_notes_2005/Lander.htm[/url] model to understand the concept. But didn't quite get how to solve this problem. I thought to consider …

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Hi everyone, Coul you please help me to find the position between Star_poso and end_posi. I have two data Data 1: Num Posi 1 2 2 5 3 9 4 16 5 19 .. .. Data 2: Num Star_posi End_posi 1 1 10 2 15 18 3 26 30 .. ... ... I want to identifi Data 1 contain in Data 2 or not? I make the script with perl in below but I just only sort with the Sta_posi. I hope I can check Data 1 between Star_posi and end _posi. I would appreciate if you could give some …

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I posted a similar thread back in Nov and got some great help. I'm modifying the code to be useful to not only compare multiple columns from two separate files, but also to classify each line from @hairpin to determine if the parameters fall within any of the ESThits, outside of them, or overlap with them. I think the script is good, but I'm very much a newbie and am getting some errors I can't figure out how to debug. Below is the code, sample data, and the errors, but if a debugger could solve my problem, please tell me …

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This is very much a bioinformatics problem, so any bioinformaticians familiar with the eUtilities of the NCBI, your help would be much appreciated. I have the following code to get links from a Pubmed search: [CODE]use Bio::DB::EUtilities; my $factory = Bio::DB::EUtilities->new(-eutil => 'elink', -email => 'mymail@foo.bar', -dbfrom => 'pubmed', -cmd => 'llinks', -id => [qw( 21330134)]); while (my $ls = $factory->next_LinkSet) { my ($id) = $ls->get_ids; # these are evaluated per id by default print "ID:$id\n"; while (my $linkout = $ls->next_UrlLink) { print "\tProvider: ",$linkout->get_provider_name,"\n"; print "\tLink : ",$linkout->get_url,"\n"; } }[/CODE] I want to query Pubmed Central so that I …

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How do you write a Python program that takes DNA sequence and give number of ORFs found in the sequence?

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Hi guys, How do i extract a sequences from a fasta file by taking the start and end position from a gene predicted file: here the example the file with the orf statistics is my predicted file and for example the start position for the first orf is 65 and the end is 213. and the fasta file i'm going to search those position is the other one my predicted file looks like this >Seq1 [organism=S.burgodofry... orf00001 65 213 +1 2.93 orf00002 799 2328 +1 7.09 orf00003 2331 3437 +3 6.09 orf00004 3457 4044 +1 6.15 >Seq2 [organism=S.burgodofry... orf00001 55 …

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The End.