This is the main help text for using the European
Bioinformatics Institute fasta3 email server.
The fasta3 (1) program provides rapid and sensitive
single protein or nucleic acid sequences against protein or
nucleic acid sequence databases.
The following databases are available. These are
recent and up-to-date databases produced at the EBI.
Name Description Sequence Input
SWALL SWALL NON-REDUNDANT Protein protein
SWISSPROT SWISS-PROT Protein Database -"-
SWNEW Updates to SWISS-PROT -"-
TREMBL TREMBL (Translated EMBL) -"-
TREMBLNEW TREMBLNEW -"-
EMBL The EMBL Database nucleic
EFUN EMBL Fungi -"-
EINV EMBL Invertebrates -"-
EHUM EMBL Human -"-
EMAM EMBL Mammalian -"-
EORG EMBL Organelles -"-
EPHG EMBL Phages -"-
EPLN EMBL Plants -"-
EPRO EMBL Prokaryote -"-
EROD EMBL Rodents -"-
ESTS EMBL STSs -"-
ESYN EMBL Synthetic -"-
EUNA EMBL Unclassified -"-
EVRL EMBL Viral -"-
EVRT EMBL Vertebrates -"-
EEST EMBL ESTs -"-
EGSS EMBL Genome Survey Sequences -"-
EHTG EMBL High Throughput Genome
EMNEW EMBL New (Updates) -"-
EMALL EMBL + EMBL New (Updates) -"-
Using the fasta email server
Using fasta through email is simply. Send a properly
formatted normal mail message to FASTA@EBI.AC.UK and wait for
the results to drop into your mailbox. Please, don't send
interactive messages, the software can't handle them!
The Input Format
Since blast through email is an automatic process
human intervention it only understands a limited set of
commands. Thus you have to adhere to a well-defined syntax,
which is pretty easy to learn and understand and should not
cause any problems. Some general rules are:
-Your mail message must contain only one command per line.
-There is only one mandatory command, SEQ. All the
commands are optional, and default values will be used
whenever they are not specified.
-You can use both uppercase and lowercase characters,
-The order of the commands is not important, but
that SEQ is the last one, since everything following this
line will be treated as a sequence (see below).
-Blank lines or space characters are accepted.
Here is a list of valid commands that are accepted
You know what it's for, don't you ?
This will normally not be required but if you want to
email server to send results somewhere else type that
email address here.
If you want to identify your search with a title please
type that description here:
LIB can be one of the following (the default
is EMALL for DNA sequences or SWALL for protein sequence):
Please referr to the list of available databases above for
the names and descriptions of databases you may use.
Your sequence itself.
This is required in order to tell the server program where the
sequence ends. Please see the SEQ command for an example.
EXAMPLE OF A SIMPLE SUBMISSION
TITLE My Sequence
The following commands are not compulsory. Defaults
generated with the mail server so you do not have to include
these in your mail if you do not wish to do so.
You may decide to use another matrix from the default
blosum62. Specify the name of the matrix here.
Word (also know as ktup) size. This is the size of
words that will be used during the comparison. For
protein and nucleic acid searches the defaults are 2
and 6 respectively. These values may be set smaller.
This will increase the sensitivity of the search but
dramatically increase the search time. We recommend you
use the default values.
The number of alignments that will be returned in the
output file. The default is set to 25.
Setting this option to any number available in the menu
allows you to set to maximum number of reported scores
in the output file. The default is 50.
This is nucleic acid only option which tells the
program to search the reverse complement of your DNA
This will make the program include in it's output a
histogram. Fasta3 calculates two scores called Init1
and Initn for each comparison between the query
sequence and sequences in the database. The histogram
show how many comparisons were observed with a certain
(1) W. R. Pearson
and D. J. Lipman (1988),
"Improved Tools for Biological Sequence Analysis",
PNAS 85:2444- 2448,
W. R. Pearson (1990),
"Rapid and Sensitive Sequence Comparison with
FASTP and FASTA",
Methods in Enzymology 183:63-98.
Fasta3 and Blast services at the EBI
Rodrigo Lopez EMBL Outstation,
The European Bioinformatics Institute.
embnet.news Vol. 7.1 (1997)
European Bioinformatics Institute
Services Programme (Support)
Wellcome Trustt Genome Campus
Hinxton, Cambridge CB10 1SD, UK
Tel: +44 (0) 1223-494444
Fax: +44 (0) 1223-494468
William R. Pearson
Department of Biochemistry
Box 440, Jordan Hall
U. of Virginia