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Other Alignment Formats (MSF)
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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.