A. Protein Sequence: Difference between revisions

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'''A1. Fasta format.'''  
<div><u><span><span><span style="font-size: 13pt">'''A1. "Fasta" format'''</span></span></span><span style="font-size: 11pt"> </span></u></div><div><u><span style="font-size: 11pt" /></u><span style="font-size: 11pt">The first line should start with '&gt;'. Next one or more </span>l<span style="font-size: 11pt">ines contain sequence in 1-letter code.</span></div><div>&nbsp;</div><div><span><font size="2">&nbsp;</font></span></div><div><font size="2">Example_A1:</font></div><pre><span><span><span style="font-size: 13pt">'''<div><font size="2">&gt;&nbsp;</font></div><div><font size="2">MDSKEVLVHVKNLEKNKSNDAAVLEILHVL</font></div><div><font size="2">DKEFVPTE KLLRETKVGVE VNKFKKSTN</font></div><span style="font-size: 12pt">VEISKLVKKMISSWKDAIN&nbsp;&nbsp;&nbsp; </span>'''</span></span></span></pre><div><span><span><span style="font-size: 13pt"</span></span></span>&nbsp;</div><div><u><span><span><span style="font-size: 13pt">'''A2. "Standard" format'''</span></span></span><span style="font-size: 11pt">.&nbsp;&nbsp;</span></u></div><div><span style="font-size: 11pt">Each line contains name of one residue in 3-letter code</span> <span style="font-size: 11pt">and optionally the residues ID. (Only residue ID of the first residue is used).</span></div><div>&nbsp;</div><div><font size="2">Example_A2.1 (position ID is not specified)</font></div><div>&nbsp;</div><pre><font size="2">GLN</font>
<font size="2">GLY
<span lang="EN-CA">GLN</span>


<span lang="EN-CA">GLY</span>
The first line shoul start with '&gt;' symbol.


<span lang="EN-CA">HIS</span>
Next one or more lines contain sequence in 1-letter code.


<span lang="EN-CA">MET</span>
<br>


<span lang="EN-CA">PRO</span>
<br>
<div><font size="2">Example_A1:</font></div><div>&nbsp;</div><div><font size="2">&gt;&nbsp;</font></div><div><font size="2">MDSKEVLVHVKNLEKNKSNDAAVLEILHVL</font></div><div><font size="2">DKEFVPTE KLLRETKVGVE VNKFKKSTN</font></div><div><font size="2">VEISKLVKKMISSWKDAIN<span>&nbsp;&nbsp;&nbsp; </span></font></div><div>&nbsp;</div>
<br>


<span lang="EN-CA">GLY</span>
<br>


<span lang="EN-CA">ILE</span>
<br>'''A2. "Standard" format.'''


<span lang="EN-CA">ILE</span>
Each line contains name of one residue in 3-lettr code and, optionally, the residue ID.


<span lang="EN-CA">TYR</span>
(only residue ID of the first residue is used to start numbering of the sequence positions).


<span lang="EN-CA">GLU</span>
<br>


<span lang="EN-CA">GLY</span>
<br>
 
<div><font size="2">Example_A2.1 (position ID is not specified)</font></div><div>&nbsp;</div><div><font size="2">GLN</font></div><div><font size="2">GLY</font></div><div><font size="2">HIS</font></div><div><font size="2">MET</font></div><div><font size="2">PRO</font></div><div><font size="2">GLY</font></div><div><font size="2">ILE</font></div><div><font size="2">ILE</font></div><div><font size="2">TYR</font></div><div><font size="2">GLU</font></div><div><font size="2">GLY</font></div><div><font size="2">LYS</font></div><div><font size="2">GLY</font></div><div><font size="2">THR</font></div><div><font size="2">ASN</font></div><div><font size="2">MET</font></div><div><font size="2">GLU</font></div><div><font size="2">....</font></div><div>&nbsp;</div><div><font size="2">Example_A2.2 (with specified all position ID):</font></div><div>&nbsp;</div><div><font size="2">GLN&nbsp; &nbsp;-3</font></div><div><font size="2">GLY &nbsp; -2</font></div><div><font size="2">HIS &nbsp; &nbsp;-1</font></div><div><font size="2">MET&nbsp;<span>&nbsp;&nbsp;0</span></font></div><div><font size="2">PRO<span>&nbsp;&nbsp; 1</span></font></div><div><font size="2">GLY&nbsp;<span>&nbsp;&nbsp; 2</span></font></div><div><font size="2">ILE<span>&nbsp;&nbsp;&nbsp; &nbsp; 3</span></font></div><div><font size="2">ILE<span>&nbsp;&nbsp;&nbsp; &nbsp; 4</span></font></div><div><font size="2">TYR&nbsp;&nbsp;&nbsp; &nbsp;5</font></div><div><font size="2">.....</font></div><div>&nbsp;</div><div><font size="2">Example_A2.3 (with specified first position ID):</font></div><div>&nbsp;</div><div><font size="2">GLN&nbsp; &nbsp;-3</font></div><div><font size="2">GLY&nbsp;</font></div><div><font size="2">HIS</font></div><div><font size="2">MET<span>&nbsp;&nbsp; </span></font></div><div><font size="2">PRO&nbsp;</font></div><div><font size="2">GLY&nbsp;</font></div><div><font size="2">ILE&nbsp;</font></div><div><font size="2">ILE&nbsp;</font></div><div><font size="2">TYR&nbsp;</font></div><div><font size="2">.....</font></div>
<st1:place w:st="on"><span lang="EN-CA">LYS</span></st1:place>
 
<span lang="EN-CA">GLY</span>
 
<span lang="EN-CA">THR</span>
 
<span lang="EN-CA">ASN</span>
 
<span lang="EN-CA">MET</span>
 
<span lang="EN-CA">GLU</span>
<span lang="EN-CA" style="font-size: 12pt; font-family: 'times new roman'; mso-fareast-font-family: 'times new roman'; mso-ansi-language: en-ca; mso-fareast-language: en-us; mso-bidi-language: ar-sa">....</span></font></pre><div><font size="2">Example_A2.2 (with specified all position ID):</font></div><div><font size="2"></font></div><pre><div><font size="2">GLN&nbsp; -3</font></div><div><font size="2">GLY&nbsp; -2</font></div><div><font size="2">HIS &nbsp;-1</font></div><div><font size="2">MET <span>&nbsp;&nbsp;0</span></font></div><div><font size="2">PRO<span>&nbsp;&nbsp; 1</span></font></div><div><font size="2">GLY <span>&nbsp;&nbsp;2</span></font></div><div><font size="2">ILE<span>&nbsp;&nbsp; 3</span></font></div><div><font size="2">ILE<span>&nbsp;&nbsp; 4</span></font></div><div><font size="2">TYR&nbsp;&nbsp; 5</font></div><div><font size="2">.....</font></div></pre><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div><font size="2">Example_A2.3 (with specified first position ID):</font></div><pre><div><font size="2">GLN&nbsp;-3</font></div><div><font size="2">GLY&nbsp;</font></div><div><font size="2">HIS </font></div><div><font size="2">MET<span>&nbsp;&nbsp; </span></font></div><div><font size="2">PRO&nbsp;</font></div><div><font size="2">GLY&nbsp;</font></div><div><font size="2">ILE&nbsp;</font></div><div><font size="2">ILE&nbsp;</font></div><div><font size="2">TYR&nbsp;</font></div><div><font size="2">.....</font></div><font size="2"></font></pre><div>&nbsp;</div>

Latest revision as of 23:49, 25 November 2009

A1. Fasta format.

The first line shoul start with '>' symbol.

Next one or more lines contain sequence in 1-letter code.



Example_A1:
 
> 
MDSKEVLVHVKNLEKNKSNDAAVLEILHVL
DKEFVPTE KLLRETKVGVE VNKFKKSTN
VEISKLVKKMISSWKDAIN   
 




A2. "Standard" format.

Each line contains name of one residue in 3-lettr code and, optionally, the residue ID.

(only residue ID of the first residue is used to start numbering of the sequence positions).



Example_A2.1 (position ID is not specified)
 
GLN
GLY
HIS
MET
PRO
GLY
ILE
ILE
TYR
GLU
GLY
LYS
GLY
THR
ASN
MET
GLU
....
 
Example_A2.2 (with specified all position ID):
 
GLN   -3
GLY   -2
HIS    -1
MET   0
PRO   1
GLY    2
ILE      3
ILE      4
TYR     5
.....
 
Example_A2.3 (with specified first position ID):
 
GLN   -3
GLY 
HIS
MET  
PRO 
GLY 
ILE 
ILE 
TYR 
.....
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