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Proteomics website

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Proteomics website

Postby dnaproteinweb » Thu Feb 11, 2010 12:07 am

Hi all, I'm new here but just wanted to let people know about a new website (www.dnatoprotein.com) I made that lets people translate DNA into protein and displays the output of both with the numbering from both sequences. It also lets you count amino acids in a sequence. If you ever do this kinda stuff, check it out, it may save you some time
-Johnny
www.dnatoprotein.com
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Postby JackBean » Thu Feb 11, 2010 12:07 pm

IMHO SwissProt good enough for such things and has little more tools ;)
http://www.expasy.ch/tools/
http://www.biolib.cz/en/main/

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Postby dnaproteinweb » Thu Feb 11, 2010 4:06 pm

Swiss Prot does not output the number of amino acid with the number of dna and have both of them aligned with the numbers. Nor does it allow the easy counting of amino acids. There are many times in construct design where you need both :)
-Johnny
Last edited by JackBean on Thu Feb 11, 2010 6:56 pm, edited 1 time in total.
Reason: no need to post link everytime
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Postby JackBean » Thu Feb 11, 2010 6:57 pm

Do you really need to count both DNA and AAs?
http://www.biolib.cz/en/main/

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Postby dnaproteinweb » Fri Feb 12, 2010 6:43 am

Technically no but you do need either. Swissprot doesn't give numbered output of either. It is also convenient to see both number sets along with which codon codes for which amino acid
-Johnny
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Postby JackBean » Fri Feb 12, 2010 8:29 am

I'm not sure, what you actually want, but what about this one?
http://searchlauncher.bcm.tmc.edu/seq-u ... frame.html
http://www.biolib.cz/en/main/

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Postby dnaproteinweb » Fri Feb 12, 2010 5:12 pm

If I have a gene and I want to see what amino acid is at position 140 of the protein corresponding to the gene, if I run that program, it doesn't tell me what amino acid is at position 40. It doesn't tell me what DNA codes for position 40 or the DNA number that codes for that. I wanted a program that would give you a map of the number of each amino acid and the number of DNA that corresponds to it. So you can look through and say "ok, I've got a EF-hand looking domain between amino acids 45-55". "this corresponds to DNA numbers so and so". If I make a primer to get rid of DNA numbers so and so I will be able to make a protein product without the EF-hand. Also, I wanted a program that would count amino acids so that if a paper refers to amino acid 160 and you just have the protein sequence or gene, you can put it into the program and you can easily locate 160 and see what other residues are around it to see if it's part of any motif
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Postby JackBean » Fri Feb 12, 2010 7:37 pm

IMHO anything of that can do any sequence viewer like BioEdit...
http://www.biolib.cz/en/main/

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Postby mith » Fri Feb 12, 2010 9:47 pm

Your tool needs more features. Right now, its functions are pretty generic.
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