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GeSeq - Annotation of Organellar Genomes


GeSeq has been developed for a rapid and accurate annotation of organelle genomes, in particular chloroplast genomes.

 

Please take a look at our documentation which includes a quickstart section and do not hesitate to report bugs or suggestions for improvements by email.


Hoover over buttons for tips. To load an example job, press "Example" in the "Actions" field.


 

FASTA file(s) to annotate
Filelist

 

Sequence source

Options

Generate multi-GenBank

Generate multi-FASTA

Generate codon-based alignments

   Include references

Annotation

Annotate plastid IR

BLAT protein search

Identity

Predict RNA editing sites

BLAT rRNA, tRNA, DNA search

Identity

Find short matches (12 nucleotides)

HMMER profile search

Embryophyta chloroplast (CDS + rRNA)

3rd Party tRNA annotators

ARAGORN v1.2.38

Genetic code

Max intron length

bp

Options

Allow overlaps

Fix intron

Report low scoring tRNAs

Additional command line parameters:

ARWEN v1.2.3

Search mode

Genetic code

Mammalia Mitochondrial

Additional command line parameters:

tRNAscan-SE v1.3.1

Search mode

Genetic code

Max intron + V-loop length

bp

Cut-off score for reporting tRNAs

Additional command line parameters:

tRNAscan-SE v2.0

Sequence source

Search mode

Genetic Code

Cut-off score for reporting tRNAs

Score and report output options

Disable pseudogene checking

Display detailed prediction output

Show origin of first-pass hits

Show primary and secondary structure components to scores

Additional command line parameters:

BLAT Reference Sequences

Server References

Add NCBI RefSeq(s)
no RefSeq selected

 

MPI-MP chloroplast references

(Embryophyta CDS + rRNA) 

 

Custom References

GenBank

fileflist

FASTA Nucleotide (CDS)

fileflist

FASTA Nucleotide (tRNA, rRNA, primer, other DNA or RNA)

fileflist
Actions
 

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Results 
joblist