Resonance Assignment/Abacus/Protein Sequence format: Difference between revisions

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1. Fasta format.
__TOC__


The first line shoul start with '>' symbol.  
== '''1. Fasta format.'''  ==
 
The first line should start with '>' symbol.  


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


<br>
<br>  
<pre>&gt;MDSKEVLVHVKNLEKNKSNDAAVLEILHVLDKEFVPTE
KLLRETKVGVE VNKFKKSTN VEISKLVKKMISSWKDAIN </pre>
<br>
 
Example 1:
 
&gt;MDSKEVLVHVKNLEKNKSNDAAVLEILHVLDKEFVPTE KLLRETKVGVE VNKFKKSTN VEISKLVKKMISSWKDAIN
 
<br>
 
<br>
 
<br>
 
2. "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).
 
<br>
 
<br>
 
<br>


Example 2.1 (position ID is not specified)
''Example 1.1:<br>''
<pre>&gt;
MDSKEVLVHVKNLEKNKSNDAAVLEILHVLDKEFVPTE
KLLRETKVGVEVNKFKKSTNVEISKLVKKMISSWKD </pre>


GLN GLY HIS MET PRO GLY ILE ILE TYR GLU GLY LYS GLY THR ASN MET GLU ....  
== <br>'''2. "Standard" format.'''  ==


Example 2.2 (with specified all position ID):
Each line contains name of one residue in 3-letter code and, optionally, the residue ID.  


GLN -3 GLY -2 HIS -1 MET 0 PRO 1 GLY 2 ILE 3 ILE 4 TYR 5 .....  
(Only residue ID of the first residue is used to start [[FMCGUI objects#Protein_sequence|numbering of sequence positions]].  


Example 2.3 (with specified first position ID):
<br>


GLN -3 GLY HIS MET PRO GLY ILE ILE TYR .....
''Example 2.1.'' (position ID is not specified):
<pre>GLN  
GLY
HIS
MET
PRO
GLY
ILE
ILE
TYR
GLU
GLY
.... </pre>
''Example 2.2.'' (with specified all position ID):
<pre>GLN  -3
GLY -2
HIS -1
MET   0
PRO   1
GLY   2
ILE   3
ILE   4
TYR   5
..... </pre>
''Example 2.3.'' (with specified first position ID):
<pre>GLN  -3
GLY 
HIS
MET
PRO
GLY
ILE
.....</pre>

Latest revision as of 23:34, 5 January 2010

1. Fasta format.

The first line should start with '>' symbol.

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


Example 1.1:
 

>
MDSKEVLVHVKNLEKNKSNDAAVLEILHVLDKEFVPTE
KLLRETKVGVEVNKFKKSTNVEISKLVKKMISSWKD


2. "Standard" format.

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

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


Example 2.1. (position ID is not specified): 

GLN 
GLY 
HIS 
MET 
PRO 
GLY 
ILE 
ILE 
TYR 
GLU 
GLY 
....

Example 2.2. (with specified all position ID): 

GLN  -3
GLY  -2 
HIS  -1 
MET   0 
PRO   1 
GLY   2 
ILE   3 
ILE   4 
TYR   5 
.....

Example 2.3. (with specified first position ID): 

GLN  -3
GLY  
HIS
MET
PRO
GLY
ILE
.....
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