From NBRF,EMBL,GENBANK TO FASTA-FORMAT

frist at ccu.umanitoba.ca frist at ccu.umanitoba.ca
Mon Oct 21 16:26:46 EST 1991


In article <CMM.0.90.2.688039905.geirha at nautsund.ifi.uio.no> geirha at ifi.uio.no (Geir Egil Hauge) writes:
>
>I want a public domain programme (SUN OR PC) that converts NBRF(PIR)
>and/or EMBL(PROT) and/or GenBank and/or EMBL(NUC) entries to the
>Pearson/FASTA-format.
>
>Please tell me where I can get such programmes from.
>
>Thanks in advance.
>
>Geir Egil Hauge

===========================================================
                    X    Y    L    E    M
===========================================================
XYLEM is a package of tools designed to exploit the Unix
environment to enable the user to identify, extract and
manipulate data from major databases such as GenBank, EMBL and
PIR. Fundamental to the power of these programs is the ability to
perform operations on groups of sequences, represented by names
or accession numbers which function as virtual database subsets.
The most powerful program is GETOB, which parses
GenBank/EMBL/DDBJ Features Table expressions to extract features
(eg. mRNA, sig_peptide, intron) from lists of entries. Additional
programs perform operations such as translation or randomization
of datasets, and formatting of multiply-aligned sequences for
publication. XYLEM is compatible with the Fristensky Sequence
Analysis Package, and the Pearson FASTA programs.

FTP: /var/spool/ftp/pub/psgendb/xylem.tar.Z   at ccu.umanitoba.ca
                                                 (130.179.16.8) 

NOTE: Because of inconsistencies in the way PIR now handles ACCESSION
numbers, the program that re-formats PIR is currently in two different
forms: one for PIR1 & PIR2, and the other for PIR3. I will include
both forms in the FTP .tar.Z file by tomorrow. Ultimately, I will
replace these programs with a single  version that handles all cases.
 
B.F.

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