# Block Formatter Help

Block formatter will format a multiple sequence alignment to the block format used in the Blocks Database. You can obtain multiple sequence alignments by various methods. A number of programs for multiple alignment are available on the WWW. One such program is Block Maker. It finds ungapped local multiple alignments (blocks) in groups of related protein sequences. The BlockMaker output is already in the block format.

The minimal input is the aligned sequence segments, all the other data can be found or given arbitrary values.

The header fields

- The ID field is a short identifier for sequences in the alignment.
  Example - "Phosphorylases".

- The Accession field is for the block name . It should be 7 or 8 characters long. It is recommended that the first 7 characters will designate the block family or group and the last character will be used to number different blocks in that group (using upper case letters A-Z).
  Examples - "TR1421_A", "TR1421_B", "Transpo".

- The minimal and maximal distance from the previous block (or from the beginning of the sequences if this is the first block) is the number of amino acids between the block and the previous one (or sequences start).
  Example - "5", "34".

- The Description field is for the description of the group of sequences from which the block was made.
  Example - "'Homeobox' domain proteins".

- The Alignment method should shortly describe how the alignment was made or found.
  Examples - "Manual alignment", "MACAW", "ClustalW", "Prot. Sci. 12 p345, 87'".

- The alignment width specifies how wide (or long) is the alignment.
  Example - "32".

- The number of sequences is how many sequences are in the alignment.
  Example - "11".

All the previous fields are optional. Their values could be given by the formatting program (either by default or from the multiple alignment).

The multiple alignment fields

- The sequence names should not be longer than 10 characters and be unique.
  Examples - "RECA_ECOLI", "S67853_A", "PCR#543"

- The positions of the aligned sequence segment are their offset from the begining of the sequence. Every position should be in a separate line. Avoid empty lines.
  Example - "67"

The names and sequence position of each aligned sequence segment in the multiple alignment will be given by the program if nothing is entered in these fields.

- This field must be filled.
  The aligned sequences should be in the amino acids single letter code. Use "-" for gaps, "X" for unknowns, and "*" for stop codons. All other characters (numbers, spaces, punctuation marks) will be ignored. Every segment in the alignment must be the same length and equal to the alignment width.
  Examples - "NAQKLMRYTK", "G--GWTEQL", "ADSEXXHYTT*"

  The sequences can be given each on a separate line (avoiding empty lines) or in the FASTA format. Each sequence in the fasta format is headed by a line begining in a '>' character. The string following this character will be taken as the sequence name. The following lines contain the sequence until the next sequence header line. Thus you can specify both sequences and their name in the sequence field if you use the FASTA format. In this format a sequence can be in more than one line.
  The readseq program can transform many sequence formats to the FASTA format.

Examples FASTA format -

    >vde_yeast vacuolar ATPAse 19 aa
    DYYGIT
    LSDDSD
    HQFLLAN

    >vde_cantr another yeast
    1  NYYGITLAE
    10 ETDHQFLLS
    19 N
    >reci_myctu (sequence can be in lower or upper case)
    r a r t f
    d l e v e
    e l h t l
    v a e g
    >reci_mycle (sequence can be on one line or more)
    SMNRFDIEVEGNHNYFVDG
    >dpi1_theli (only first word in this line is read as sequence name)
    EGYVYDLSV
    EDNENFLVGF

    >dpi2_theli (header lines MUST start with a '>')
    EGYV
    YDIE
    VEET
    HRFF
    ANN

basic format -

    DYYGITLSDDSDHQFLLAN
    NYYGITLAEETDHQFLLSN
    RARTFDLEVEELHTLVAEG
    SMNRFDIEVEGNHNYFVDG
    EGYVYDLSVEDNENFLVGF
    EGYVYDIEVEETHRFFANN

An example of a possible output -

    ID   Inteins; BLOCK
    AC   vde_yea; distance from previous block = (98,190)
    DE   Protein introns (inteins).
    BL   gibbs; width=19; seqs=6;
     vde_yeast ( 430) DYYGITLSDDSDHQFLLAN  90
     vde_cantr ( 447) NYYGITLAEETDHQFLLSN  84
    reci_myctu ( 417) RARTFDLEVEELHTLVAEG 100
    reci_mycle ( 342) SMNRFDIEVEGNHNYFVDG  95
    dpi1_theli ( 513) EGYVYDLSVEDNENFLVGF  83
    dpi2_theli ( 367) EGYVYDIEVEETHRFFANN  74
    //

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Page last modified August 1996