Re: sequence composition

[changrong ge]

Tack så mycket, I will check that website The output is the percentage of each amino acid in the protein. For example, protein A is 100 amino acid long, in which there are 10 lysine, then the output for lysine is 0.1, the same rule for the other amino acids. In the output, the first row should be amino acid name, then second row, third row,..... are the protein names, that means the second row is protein A, third row is protein B, and so on. There are also 21 columns, the first column are a list of protein names, then the following 20 columns are the amino acid percentage for all the proteins. Looks like the figure below: Thanks Have a nice day Changrong On 2010-12-01 09:59, Shlomi Fish wrote: Hi, On Wednesday 01 December 2010 10:44:17 Changrong Ge wrote: Hi, I am quite new to this perl language-I am from biochemistry field. Now trying to write a script for my current work but could not make it. The idea is to calculate the composition (percentage) of amino acids in a protein sequence. Input is a series of fasta format (protein sequence) output is a tab delimited format like below: Name A T C D N Q E ....... protein1 0.23 0.40 0.20 . .. protein2 0.52 0.01 . ... protein3 ...... Please go to http://perl-begin.org/ and see if any of the resources there help you. I'm not initimately familiar with the Fasta format - http://en.wikipedia.org/wiki/FASTA_format - but what should the output contain exactly? Could somebody help me with this? I tried reading some books like perl for bioinformatics, but still not into it. Thanks in advance. Changrong Regards, Shlomi Fish