[Biojava-l] Gsoc Amino acids physico-chemical properties calculation

[Peter Troshin]

Dear Alex,

The BioJava projects all have some elements of Chemistry and/or 
Molecular Biology in them. So some understanding of these areas is 
necessary. If you do not possess them, then it is going to be hard to 
produce a competitive project plan. So you may be better off applying to 
pure Java projects. Completing the coding exercise will not be enough to 
get through!

Kind regards,
Peter

On 25/03/2011 18:06, Alexandru Paiu wrote:
> Hi Peter
>
> It's me again Paiu Alexandru from Romania .
>
> I've started to study for 2 days about amino acids , but i didn't find
> anything in romanian about the properties I have to implement for this
> project . I found only about amino acids in general . I went to the
> university library to find books about amino acids but i wasn't so lucky .
> I'm really stucked in getting some information about that properties .
>
> I found on wikipedia formulas and some informations about every method , but
> I really can't understand exactly what is every formula trying to do . I'd
> need some concrete examples for every method I have to implement . There are
> to many abbreviations that I don't understand . I tried to get some help
> from some friends that are studying pharmacy , but they couldn't help me .
> I studied that tool
> http://expasy.org/tools/<http://expasy.org/tools/protparam-doc.html>,
> but i haven't figured out yet exactly how those methods work (which
> are
> the inputs for each method and how they obtain those outputs )
>
> I've started to work the goals on Selection criteria . I've finished the
> first 2 , now i'm working on using threads .
> I'll use threads for taking multiple lines from the input file . Each Thread
> will take a line at a time , will take the 2 strings separated by '\t' and
> will be applied  StringOverlapFinder over the 2 Strings . In
> StringOverlapFinder i look for the last 5 characters of String 1 in String 2
> . If it isn't found i print String 1 . If is found an overlap , then there
> are more cases to take care of . Some examples :
> Ex 1 : x = "abcdefghijklm" and y = "hijklmnopqrst" (your example)  then the
> output is =abcdefg
> Ex 2 : x="asdcsadvsasevenfiveseven"  and y="sevenfivesevenasdasdas" then the
> output is = asdcsadvsa
> Ex 3: x="ascdaeseven" and y="bseven" and the output is x
>
> So after this 3 examples i've found the "right" implementation . And for
> this I'll take Ex Nr 2 , because I think it's the most complex .
> I find that the the last 5 chars (seven) is found on index 0 . I take the
> substring from y starting with index 0 and ending with the index of the
> first overlap that is 0 too . So having a null substring the program should
> stop here and the output would be asdcsadvsasevenfive . But the real output
> shoud be asdcsadvsa .
> So , after finding that this is a posible output , i should look for a
> second overlap in y . It is found at index 9 ( the second seven) . I take
> the substring again from y that starts with index 0 and end with index 8  (
> 9-1 ) and that is sevenfive . The lenght of this substring is 9 . Now i take
> another substring but this time from x . It starts from index
> (x.length()-5-9) and ends with index ( x.length()-5) . In this case this
> substrings are equall and the program will write the correct output that is
> asdcsadvsa . But before that , it should search for another possible overlap
> , but in this case there isn't one .
> In Ex Nr 3 it is found the "seven" string in y . It's taken the substring
> from y , that is "b" , and is compared with the substring from x that is "e"
> . They aren't equal so there is not an overlap . The program will look for
> another string "seven" in y , but there isn't one so the output will be x ,
> because there wasn't found any overlap .
> I hope you understand my Ideeas . I'll send to you the jar when it's
> finished
>
> Is there a deadline for this selection criteria ?
> That's it for today
>
> Best Regards ,
> Alex
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l