In Matlab

ChIP-seq is used to identify genomic segments bound by transcription factors. In a ChIP-seq experiment, you obtain the chromosome regions that the transcription factor FoxA is binding. Write a Matlab function locationtogenes(chr,start,finish,genefile) that takes a chromosome name, the start and finish of the chromosome region in base pairs, and a gene-location file; and determines which genes are located in that region. The gene-location file is a tab-delimited text file where each line contains chromosome-start-finish-genename. Find the genes whose position overlaps with the input range (the gene doesn't have to be completely enclosed in the input range to be considered overlapping; at least one nucleotide overlap is sufficient). Return these genes as a cell array. If no genes are found in an input range, return an empty cell array. An example gene-location file can be downloaded from http://sacan.biomed.drexel.edu/ftp/bmeprog/genelocs_sample.txt You should not download any files from the web in your code; you can assume that your function will be given a filename that already exists.

Sample

>> disp(locationtogenes('chr1',59000000,59247000,'genelocs_sample.txt')) 'JUN' >> disp(locationtogenes('chr1',50000000,100000000,'genelocs_sample.txt')) 'RP4-784A16.2' 'MRPL37' 'JUN' 'LRRC8C'