 |
|
| PDB -- extensions .pdb .ent .noc |
| FASTA --
extensions .fa .fst .fasta |
| PIR --
extensions .pir .ali |
| CLUSTAL --
extensions .aln |
CE -- extensions
.cea
|
| SKY --
extensions .sky |
|
| Please see the description of the PDB format at the Protein Data Bank webpage.
|
|
| Please see the description of the FASTA format at the NCBI web page.
|
|
A sequence in PIR format consists
of :
- First line starting with a ">??;" or ">??;" ('?'
stands for any character), followed by a sequence name;
- Second line containing a text description of the sequence.
Friend saves the description line in the form of
"StructureX:pdbcode:first_residue_index:chain:last_residue_index:chain:";
- One or more lines containing the sequence itself. The end
of the sequence must be marked by a "*" character.
The PIR format is also often referred to as the NBRF format.
See example for more details.
|
|
The CLUSTAL format can be described as follows:
- the word CLUSTAL should be on
the first non-space line of the file;
- the alignment is displayed in
blocks of a fixed length;
- each line in the block
corresponds to one sequence;
- the line starts with the
sequence name (of any length), followed by at least one space character;
- then the sequence is
displayed: upper or lowercase, '-' denotes gaps, residue number is
displayed optionally at the end;
- in between blocks a line shows
conservation information.
See example for more details.
|
|
A sequence in CE format is described by one line.
- A line starts from the sequence description in the form
"pdb-code:chain(last_residue_index:first_residue_index-last_residue_index)".
- The sequence starts from the position 32.
See example for more details.
|
|
The format is under development but the example can be found here.
|
