ChIP-seq is used to identify genomic segments bound by transcription factors. In
ID: 3846175 • Letter: C
Question
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.
Example:
>> disp(locationtogenes('chr1',59000000,59247000,'genelocs_sample.txt'))
'JUN'
>> disp(locationtogenes('chr1',50000000,100000000,'genelocs_sample.txt'))
'RP4-784A16.2' 'MRPL37' 'JUN' 'LRRC8C'
You may follow the pseudocode below or design & implement your own approach.
Explanation / Answer
function [ out ] = locationtogenes( chr,start,finish,genefile )
%UNTITLED Summary of this function goes here
% Detailed explanation goes here
f=fopen(genefile,'r'); %open file
out=[];
while ~feof(f)
line = fgetl(f);
locs=find(line==sprintf(' '));
if numel(locs)<3; continue; end
if strfind(line,chr)>0
chr1= line(locs(1)+1 : locs(2)-1);
if strfind(line,start)>0
start1= line(locs(2)+1 : locs(3)-1);
if strfind(line,finish)>0
finish1= line(locs(3)+1 : locs(4)-1);
if strfind(line,genename)>0
genename= line(locs(4)+1 : locs(5)-1);
break;
if start1==start && finish1==finish
out=genename
break;
end
end
end
end
end
end
end