Protein Fragment Finder v1.0

2015

James Dean (dean.james.r@gmail.com)



This program was made to help cut down on the time spent searching for the protein fragments that have a particular mass.  Coded in Python 2.7; source is located in the dist folder as bioscript.py. Uses the BioPython, PyReadLine, and Numpy packages. Icon used was generated in Chimera using 2PEC (Pectate Lyase C).







How to use:

1. Calculate the potential cleavage sites for your protein

2. Paste those cleavage sites into the program, with the numbers separated by spaces and press "ENTER"

3. Paste in the full (uncut!) sequence of the protein and press "ENTER"

4. Paste in the molecular weight you're trying to find, in Daltons, and press "ENTER"

5. You will get the closest match to the weight you were looking for, along with the first and last amino acid positions where this occurs. If you want the 2nd-best match, type "continue" when prompted and press "ENTER". Repeat this process for the 3rd/4th/etc. best matches.

6. When you have enough masses found, type "stop" when prompted and press "ENTER". You will get a small table of all of your masses, along with their positions.

7. To look at another set of cleavage sites/another protein/another molecular weight, type "continue" when prompted, and follow these instructions once again from step 1. Otherwise, if you are finished, rype "done" when prompted and press "ENTER" to end the program.







Here is an example set of inputs to use in case you're unsure you are doing it right.



Cleavage sites: 

21 37 43 44 46 77 80 85 89 108 109 119 128 134 172 189 190 203 218 223 245 259 267 271 279 331 333 342 353



Full sequence: 

ATDTGGYAATAGGNVTGAVSKTATSMQDIVNIIDAARLDANGKKVKGGAYPLVITYTGNEDSLINAAAANICGQWSKDPRGVEIKEFTKGITIIGANGSSANFGIWIKKSSDVVVQNMRIGYLPGGAKDGDMIRVDDSPNVWVDHNELFAANHECDGTPDNDTTFESAVDIKGASNTVTVSYNYIHGVKKVGLDGSSSSDTGRNITYHHNYYNDVNARLPLQRGGLVHAYNNLYTNITGSGLNVRQNGQALIENNWFEKAINPVTSRYDGKNFGTWVLKGNNITKPADFSTYSITWTADTKPYVNADSWTSTGTFPTVAYNYSPVSAQCVKDKLPGYAGVGKNLATLTSTACK



Molecular Weight:

17995



If you did it right, you should get a best weight of 17995 from residues 1-172.