Specification of SAF (Simple Alignment Format)

Examples for SAF alignments

Compulsory features:

Each ROW

• 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

• 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

• 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