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

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 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.

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