(This is a database / R commands question) I wish (for my thesis work), to import tRNA data into R and have it aligned. My questions are: 1) What resources can I use for the data. 2) What commands might help me with the import/alignment. So far, I found two nice repositories that holds such data: tRNAdb at the University of Leipzig ...
I'm looking for a faster way to calculate GC content for DNA strings read in from a FASTA file. This boils down to taking a string and counting the number of times that the letter 'G' or 'C' appears. I also want to specify the range of characters to consider. I have a working function that is fairly slow, and it's causing a bottleneck...
I'm trying to do a simple genomic track intersection in R, and running into major performance problems, probably related to my use of for loops. In this situation, I have pre-defined windows at intervals of 100bp and I'm trying to calculate how much of each window is covered by the annotations in mylist. Graphically, it looks somethi...
I'm making a large number of seqlogos programmatically. They are hundreds of columns wide and so running a seqlogo normally creates letters that are too thin to see. I've noticed that I only care about a few of these columns (not necessarily consecutive columns) ... most are noise but some are highly conserved. I use something like this...
I work as support staff in a Biology research institute as a student, and Perl seems to be used everywhere. Not for every single project, but it seems that more than half the people here have a few Perl books in/on their office/desk. Why is Perl used so much in Biology? ...
EDIT: Please close this question. I asked and got an answer for it on BioStar here. In BioPerl, a sequence object can have any number of features, and each of these can have subfeatures nested within them. For example, a feature may be a complete coding sequence of a gene, and its subfeatures might be individual exons that ar...
How can I extract DNA sequence using a Perl script from genome browser (UCSC), if I have their coordinates? ...
I have a dense matrix where the indices correspond to genes. While gene identifiers are often integers, they are not contiguous integers. They could be strings instead, too. I suppose I could use a boost sparse matrix of some sort with integer keys, and it wouldn't matter if they're contiguous. Or would this still occupy a great deal of...
I'm storing contacts between different elements. I want to eliminate elements of certain type and store new contacts of elements which were interconnected by the eliminated element. Problem background Imagine this problem. You have a water molecule which is in contact with other molecules (if the contact is a hydrogen bond, there can b...
Hey guys this is my first question on here. I'm trying to make a local copy of the UniprotKB in SQL. The UniprotKB is 2.1GB, and it comes in XML and a special text format used by SwissProt Here are my options: 1) Use a SAX parser (XML) - I chose Ruby, and Nokogiri. I started writing the parser, but my initial reaction: how would I map...
My fried suggest I try to apply for a job at EMBL. I'm not bioinformatic in any way, but my friend (who by the way is a biologist working at EMBL) insists that I could adapt to the new environment as long as I have a interest in subject and am generally good at learning new things. But here is a catch. For the last 4 years I've been wor...
I have done a couple research jobs in Bio-informatics and I have used Matlab for them. Matlab had a lot of powerful tools and was easy to use. I did thinks with genome sequencing and predicting metabolic pathways. I am wondering what other people think is best? or there might not be one specific language but a few that lend themselves be...
I have a scientific data management problem which seems general, but I can't find an existing solution or even a description of it, which I have long puzzled over. I am about to embark on a major rewrite (python) but I thought I'd cast about one last time for existing solutions, so I can scrap my own and get back to the biology, or at l...
Hi there. I have a FASTA file containing several protein sequences. The format is like ---------------------- >protein1 MYRALRLLARSRPLVRAPAAALASAPGLGGAAVPSFWPPNAAR MASQNSFRIEYDTFGELKVPNDKYYGAQTVRSTMNFKIGGVTE RMPTPVIKAFGILKRAAAEVNQDYGLDPKIANAIMKAADEVAE GKLNDHFPLVVWQTGSGTQTNMNVNEVISNRAIEMLGGELGSK IPVHPNDHVNKSQ >protein2 MRSRPAGPALLLLLLF...
Hi all, I am new to Image Processing. I will use Image Processing to for Medical Images. I am searching for video lectures or any other good learning resources? Any help. Thanks in advance. Regards, Saghar Ayyaz ...
I've written a bookmarlet to open a user defined web link, in this specific case a specific genomic location in the UCSC genome broswer. javascript:d=%22%22+(window.getSelection?window.getSelection():document.getSelection?document.getSelection():document.selection.createRange().text);d=d.replace(/%5Cr%5Cn%7C%5Cr%7C%5Cn/g,%22%20,%22);if(...
How can I fetch genomic sequence efficiently using Python? For example, from a .fa file or some other easily obtained format? I basically want an interface fetch_seq(chrom, strand, start, end) which will return the sequence [start, end] on the given chromosome on the specified strand. Analogously, is there a programmatic python interf...
I want to use the P4 Python Package on a windows machine. from: [http://www.bmnh.org/~pf/p4.html][1] I have python 2.6 installed and working with numpy ready and realines.py installed. There is a win32-gbu version of GSL installed on my windows machine, from gnuwin32.sourceforge.net/packages/gsl.htm When I try to install P4, using set...
I'm trying to get the mean length of fasta sequences using Erlang. A fasta file looks like this >title1 ATGACTAGCTAGCAGCGATCGACCGTCGTACGC ATCGATCGCATCGATGCTACGATCGATCATATA ATGACTAGCTAGCAGCGATCGACCGTCGTACGC ATCGATCGCATCGATGCTACGATCTCGTACGC >title2 ATCGATCGCATCGATGCTACGATCTCGTACGC ATGACTAGCTAGCAGCGATCGACCGTCGTACGC ATCGATCGCATCGATGCTACGATC...
I'm writing a Clojure implementation of this coding challenge, attempting to find the average length of sequence records in Fasta format: >1 GATCGA GTC >2 GCA >3 AAAAA For more background see this related StackOverflow post about an Erlang solution. My beginner Clojure attempt uses lazy-seq to attempt to read in the file one record a...