Other Alignment Formats (MSF)
 


Alignment in MSF format

Often the alignment forms returned by servers most resemble the common MSF format. However, in order for the format to function correctly certain rules have to be followed. Here is an example MSF alignment


 1kit  MSF: 276  Type: P  May 06, 2004  10:56  Check: 0 ..

 Name: 3sil             Len:   276  Check: 6095  Weight:  1.00
 Name: 1kit             Len:   276  Check: 4858  Weight:  1.00
//

3sil  ---------- ---------- ---------- ---------- ----------
1kit  ALFDYNATGD TEFDSPAKQG WMQDNTNNGS GVLTNADGMP AWLVQGIGGR

3sil  ---------- ---------- ---------- ---------- ----------
1kit  AQWTYSLSTN QHAQASSFGW RMTTEMKVLS GGMITNYYAN GTQRVLPIIS

3sil  ---------- ---------- ---------- ---------- -KSVVFKAEG
1kit  LDSSGNLVVE FEGQTGRTVL ATGTAATEYH KFELVFLPGS NPSASFYFDG

3sil  EHFTD----- --QKGNTIVG SGSGGTT--- ---------- --KYFRIP--
1kit  KLIRDNIQPT ASKQNMIVWG NGSSNTDGVA AYRDIKFEIQ GDVIFRGPDR

3sil  ----AMCTTS KGTIVVFADA RHNTASDQSF IDT---AAAR STDGGKTWNK
1kit  IPSIVASSVT PGVVTAFAEK RVGGGDPGAL SNTNDIITRT SRDGGITWDT

3sil  KIAIYNDRVN SKLSRVMDPT CIVANI
1kit  ELNLTEQINV SDEFDFSDPR PIYD--

Note that there is a header file containing the sequence identifiers (1kit and 3sil) that ends with two slashes (//). After this anything on lines that begin with the sequence identifiers is treated as the aligned sequence. All leading and trailing numbers on this line should be removed therefore or they will be treated as part of the sequence. Whitespace is irrelevant. Gaps in your sequence can be dots or dashes. All lines without sequence identifiers are ignored, so you dont have to delete these.

So in order to make your alignment MSF for the purposes of this server, simply copy and paste the following above the alignment, making sure that the sequence identifiers correspond with the ones you are using:

 
 1kit  MSF: 10  Type: P  May 06, 2004  10:56  Check: 0 ..

 Name: your_query_sequence_identifier             Len:   10  Check: 0  Weight:  0
 Name: your_template_structure_identifier        Len:   10  Check: 0  Weight:  0
//

The file format recognised include FASTA, MSF, PIR, CLUSTAL, ACEDB, CODATA, EMBL, GENBANK, IG/STANFORD, NRBF, STRIDER. If you receive an error message from the server please check first with the format specifications available on the web.