Ajuda per a usar el Fasta via Email


 

Help [fasta]

Introduction
------------

This is the main help text for using the European
Bioinformatics Institute fasta3 email server.
 

The fasta3 (1) program provides rapid and sensitive scanning of
single protein or nucleic acid sequences against protein or
nucleic acid sequence databases.
 

Databases available
-------------------

The following databases are available. These are the most
recent and up-to-date databases produced at the EBI.

Name  Description   Sequence Input
--------------------------------------------------------------
SWALL          SWALL NON-REDUNDANT Protein      protein
               sequence database
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
               Sequences                        -"-
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 without any
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 other
 commands are optional, and default values will be used
 whenever they are not specified.

-You can use both uppercase and lowercase characters, or mix
 them.

-The order of the commands is not important, but make sure
 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 by email
server:

HELP
         You know what it's for, don't you ?

PATH
         This will normally not be required but if you want to
         email server to send results somewhere else type that
         email address here.
         Example:
         PATH    joe@somewhere.there

TITLE
         If you want to identify your search with a title please
         type that description here:
         Example:
         TITLE    gpr-ii-rpt

LIB
         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.
         Example:
         LIB   tremblnew

SEQ
         Your sequence itself.
         Example:
         SEQ
         MPNIPTISLNDGRPFAEPGLGTYNLRGDEGVAAMVAAIDSGYRLLDTAVNYENESEVGRA
         VRASSVDRDELIVASKIPGRQHGRAEAVDSIRGSLDRLGLDVIDLQLIHWPNPSVGRWLD
         TWRGMIDAREAGLVRSIGVSNFTEPMLKTLIDETGVTPAVNQVELHPYFPQAA
         END
 
END
         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
------------------------------

PATH joe@somewhere.there
TITLE My Sequence
LIB swall
SEQ
MMFSGFNADYEASSSRCSSASPAGDSLSYYHSPADSFSSMGSPVNAQDFC
TDLAVSSANFIPTVTAISTSPDLQWLVQPALVSSVAPSQTRAPHPFGVPA
PSAGAYSRAGVVKTMTGGRAQSIGRRGKVEQLSPEEEEKRRIRRERNKMA
AAKCRNRRRELTDTLQAETDQLEDEKSALQTEIANLLKEKEKLEFILAAH
RPACKIPDDLGFPEEMSVASLDLTGGLPEVATPESEEAFTLPLLNDPEPK
PSVEPVKSISSMELKTEPFDDFLFPASSRPSGSETARSVPDMDLSGSFYA
ADWEPLHSGSLGMGPMATELEPLCTPVVTCTPSCTAYTSSFVFTYPEADS
FPSCAAAHRKGSSSNEPSSDSLSSPTLLAL
END

The following commands are not compulsory. Defaults will be
generated with the mail server so you do not have to include
these in your mail if you do not wish to do so.
 

MATRIX
         You may decide to use another matrix from the default
         blosum62. Specify the name of the matrix here.
         Example:
         MATRIX   pam250

WORD
         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.
         Example:
         WORD 4

ALIGN
         The number of alignments that will be returned in the
         output file. The default is set to 25.
         Example:
         ALIGN   50

LIST
         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.
         Example:
         LIST  25

STRAND
         This is nucleic acid only option which tells the
         program to search the reverse complement of your DNA
         query sequence.
         Example:
         STRAND bottom

HISTOGRAM

         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
         score.
         Example:
         HISTOGRAM yes
 

References
-----------
 

       (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)

Contacts
--------

 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
 support@ebi.ac.uk
 http://www2.ebi.ac.uk/fasta3

 William R. Pearson
 Department of Biochemistry
 Box 440, Jordan Hall
 U. of Virginia
 Charlottesville, VA


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