The first part of a block-file contains the identifier codes of the sequences that are to follow. Each code is prefixed by the > symbol, codes must not contain spaces.
e.g.
>HAHU >Trypsin >A0046 >Seq1
etc.
ALSCRIPT counts the number of > symbols in the beginning of the file until a * symbol is found. The * signals the beginning of the multiple alignment which is stored VERTICALLY, thus columns are individual sequences, whilst rows are aligned positions. The * symbol must lie over the first sequence. A further star in the same column signals the end of the alignment. ALSCRIPT uses the number of > symbols at the beginning of the file to work out how many columns to read from the * position. It is therefore important that the only > symbols in the file are those that define the identifiers, and the only * symbols are those defining the start and end of the multiple alignment. The block file can contain additional text, providing that there are no more > or * symbols in the file than those used to define the identifiers or alignment start and end.
A simple, small block-file is shown here.
>Seq_1 >A0231 >HAHU >Four_Alpha >Globin >GLobin_C * ARNDLQ AAAAAA PPPPPP PP PPP WW WWW LLLLLL IIVVLL *