| Version 1 (modified by jan.aerts, 16 years ago) |
|---|
Random ideas from Jan Aerts
Mind that this is *very* incomplete. Just to help my really bad memory. As the issue is interoperability of the Bio* toolkits, we don't have to synchronise the toolkits at the object level, but rather at the interface level. So let's see if each toolkit reads and writes a GenBank/Fasta/... serialization in the same way. Input can either be an original GenBank/Fasta/... file or a dbfetch from any database.
- What should be conserved:
- Tags
- for a sequence: lower/uppercase
- What not necessarily should be conserved:
- for a sequence over multiple lines: length of each lin
Attachments
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dag1.fa
(5.6 KB) - added by jan.aerts
16 years ago.
DAG1 gene: FASTA formatted sequence
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dag1.gb
(17.9 KB) - added by jan.aerts
16 years ago.
DAG1 gene: genbank formatted file exported from NCBI
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dag1.insd
(38.6 KB) - added by jan.aerts
16 years ago.
DAG1 gene: INSD XML formatted file exported from NCBI
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dag1.asn1
(58.0 KB) - added by jan.aerts
16 years ago.
DAG1 gene: ASN.1 formatted file exported from NCBI
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dag1.gb_xml
(227.9 KB) - added by jan.aerts
16 years ago.
DAG1 gene: genbank XML formatted file exported from NCBI (probably?)
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aj224122.asn1
(17.9 KB) - added by jan.aerts
16 years ago.
AJ224122 in ASN1 format as downloaded from NCBI
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aj224122.fa
(3.9 KB) - added by jan.aerts
16 years ago.
AJ224122 in FASTA format as downloaded from NCBI
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aj224122.gb
(8.9 KB) - added by jan.aerts
16 years ago.
AJ224122 in genbank format as downloaded from NCBI
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aj224122.gb_xml
(68.3 KB) - added by jan.aerts
16 years ago.
AJ224122 in genbank XML format as downloaded from NCBI
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aj224122.insd
(19.5 KB) - added by jan.aerts
16 years ago.
AJ224122 in INSD format as downloaded from NCBI
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aj224122.swiss
(7.8 KB) - added by heikki
16 years ago.
AJ224122 translation (DOF37_ARATH/Q43385) in swiss-prot format as downloaded from UniProt?
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dag1-biojava.fa
(5.7 KB) - added by markjschreiber
16 years ago.
biojava roundtrip of fasta
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aj224122-biojava.fa
(3.9 KB) - added by markjschreiber
16 years ago.
biojava roundtrip of fasta
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aj224122-biojava.gb
(9.1 KB) - added by markjschreiber
16 years ago.
biojava roundtrip of genbank
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aj224122-biojava.insd
(22.6 KB) - added by markjschreiber
16 years ago.
biojava roundtrip of ISNDseq
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aj224122.embl
(9.1 KB) - added by markjschreiber
16 years ago.
Correct version of EMBL file
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aj224122.EMBL.xml
(14.9 KB) - added by markjschreiber
16 years ago.
EMBLxml format
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aj224122.uniprot.xml
(17.2 KB) - added by markjschreiber
16 years ago.
uniprot xml
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aj224122-biojava.insd.xml
(23.6 KB) - added by markjschreiber
16 years ago.
biojava round trip of INSDseq
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Main.java
(4.7 KB) - added by markjschreiber
16 years ago.
Roundtrip program for biojava
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derby-biosql.sql
(27.7 KB) - added by markjschreiber
16 years ago.
DERBY schema for BioSQL
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aj224122-biojava.embl
(9.2 KB) - added by holland
16 years ago.
biojava embl round-trip
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aj224122-biojava.swiss
(7.8 KB) - added by holland
16 years ago.
biojava uniprot round-trip
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aj224122-biojava.uniprot.xml
(18.0 KB) - added by holland
16 years ago.
biojava uniprotxml round trip
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aj224122-bioruby.embl
(8.9 KB) - added by jan.aerts
16 years ago.
bioruby roundtrip for EMBL format
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roundtrip_bioruby.rb
(161 bytes) - added by jan.aerts
16 years ago.
Ruby script for roundtrip (i.c. EMBL)
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bioruby_aav50056_fasta_annotated.png
(108.3 KB) - added by jan.aerts
16 years ago.
Annotated picture of a FASTA entry
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bioruby_ab09071_embl_annotated.png
(92.0 KB) - added by jan.aerts
16 years ago.
Annotated picture of an EMBL entry
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bioruby_ab09071_gb_annotated.png
(124.9 KB) - added by jan.aerts
16 years ago.
Annotated picture of a GenBank? entry
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bioperl_convert.pl
(1.6 KB) - added by heikki
16 years ago.
Bioperl script fr roundtriping EMBL, GenBank? and Swiss-Prot files
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aj224122-bioperl.fa
(3.9 KB) - added by heikki
16 years ago.
bioperl processed fasta file
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aj224122-bioperl.gb
(8.9 KB) - added by heikki
16 years ago.
bioperl processed Genbank file
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aj224122-bioperl.swiss
(7.8 KB) - added by heikki
16 years ago.
bioperl processed swissprot file
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aj224122-bioperl.embl
(8.9 KB) - added by heikki
16 years ago.
bioperl processed EMBL file
