Specification of SAF (Simple Alignment Format)

Examples for SAF alignments

Compulsory features:

Each ROW

Each row contains two columns, separated by blanks or tabulators.

FIRST COLUMN:
name (protein identifier, shorter than 14 characters, names should be uniqe, no blanks in names accepted)
SECOND COLUMN:
one-letter sequence (any number of characters) insertions: dots (.), hyphens (-), or additional blanks.
Note: blanks in sequences are ignored, the first residue (one-letter code), or the first insertion (.) will be taken as begin of the sequence line.

EXAMPLE: t2_11751 GGAPTLPETL NVAGGAPTLP ETLNVAGGAP TLPETLNV

Each BLOCK

Blocks contain the sequences of the proteins aligned to the guide sequence (first sequence) between residues N1 and N2.

FIRST ROW:
The first row must be the guide sequence.
SECOND - N-th ROW:
The sequences aligned in the region between residues N1 and N2 of the guide sequence. Note:
- the order of sequences may differ between blocks
- NOT all 2-N sequence have to occur in each block
- C-terminal insertions may be left out for sequences 2-N (but NOT for the guide sequence)
- BUT: whenever a sequence is present, it should have dots for insertiother than blanks at the N-term of each row
COMMENTS:
- rows beginning with a hash (#) will be ignored
- rows containing only blanks, dots, numbers will also be ignored (in particular you may insert lines with residue numbers)

EXAMPLE: t2_11751 GGAPTLPETL NVAGGAPTLP ETLNVAGGAP TLPETLNV name_22 .......... .......... .......... ........ name_1 GGAPTLPETL NVAGGAPTLP ETLNVAGGAP TLPETLNV name_2 .......... NVAGGAPTLP

WARNING

The 'freedom' provided by SAF has various consequences:

identical names in different rows of the same block are not identified. Instead, whenever this applies, the second, (third, ..) sequences are ignored. For example: t2_11751 EFQEDQENVN name-1 ...EDQENvk name-1 GGAPTLPETL
will be interpreted as: t2_11751 EFQEDQENVN name-1 ...EDQENvk
wheras: t2_11751 EFQEDQENVN name-1 ...EDQENvk name_1 GGAPTLPETL
is interpreted as 3 different sequences (note the usage of a hyphen (-) in the name of the second protein, and that of an uncerline (_) in the name of the third.
spelling mistakes in the names will not be detected

missing lines will also not be detected, e.g., you may want to give: t2_11751 GGAPTLPETL name_1 DEAPTLPETL t2_11751 NVAGGAPTLP name_1 SEGTTAPTLS t2_11751 ETLNVAGGAP name_1 E...VAGGAP
and you may actually have given t2_11751 GGAPTLPETL name_1 DEAPTLPETL t2_11751 NVAGGAPTLP t2_11751 ETLNVAGGAP name_1 E...VAGGAP
then PP would use the following alignment t2_11751 GGAPTLPETL ETLNVAGGAP name_1 DEAPTLPETL SEGTTAPTLS
instead of t2_11751 GGAPTLPETL NVAGGAPTLP ETLNVAGGAP name_1 DEAPTLPETL SEGTTAPTLS E...VAGGAP