BAC and Gene Annotator
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Test Sequences
Welcome to ACPFG Bioinformatic's BAC and Gene Annotator.

This sevice performs automatic annotation for either single BAC sequences or multiple fasta files containing a collection of genes / ESTs of interest.

When annotating a BAC, this system uses Genscan to identify potential genes. These genes are then compared against sequences in the EMBL and UniProt databases to identify potential orthologues. If chosen, the system can identify syntenic regions on a number of reference genomes and provides links to external sites which provide more information.

When annotating a list of genes, the sequences are compared against the EMBL and UniProt databases and a table of potential orthologues is produced.

All input sequences are masked with RepeatMasker before annotation begins.
1
Please enter a valid email address:


(This must be a valid email address. The results from the pipeline will be sent to this email address.)



2
Type of sequence data submitted:

BAC - A single BAC in FASTA format
GENES - A list of genes/ESTs (multiple FASTA)



3
Sequence data:

Either: Select the sequence file to upload:

Otherwise: Enter a sequence in FASTA format:

For BAC sequences, please select the closest species (used with Genscan):
 

Advanced Options (BACs only)
  Reference Genome Blast (For BAC submissions only)
You can compare your sequence with the following genomes:
  Arabidopsis thaliana
  Human
  Mouse
  Rice
 
If you would like to compare your sequence with another genome, please contact .
 
  Run Wu-Blast (For BAC submissions only)
You can compare your sequence against GenBank and UniRef 90 databases:

Note: Due to the intense nature of this option, the job duration may be extended by up to 48 hours if one or more of these options is chosen.
  Wu-Blast submitted BAC against GenBank
  Wu-Blast submitted BAC against UniRef90
 
  Repeat Masking Options (For BAC submissions only)
The submitted BAC sequence can be masked with RepeatMasker if one or more of the Wu-Blast options are chosen.

You can use the following repeat libraries for sequence masking:
  Arabidopsis (TIGR Arabidopsis GSS Repeats) Maize (TIGR Zea GSS Repeats)
  Brassica (TIGR Brassica GSS Repeats) Human (Repbase humrep)
  Soybean (TIGR Glycine GSS Repeats) Funghi (Repbase fngrep)
  Lotus (TIGR Lotus GSS Repeats) Mamalian (Repbase mamrep)
  Tomato (TIGR Lycopersicon GSS Repeats) Rodent (Repbase rodrep)
  Medicago (TIGR Medicago GSS Repeats) Zebra fish (Repbase zebrep)
  Rice (TIGR Oryza GSS Repeats) Nematode worm (Repbase nemrep)
  Sorghum (TIGR Sorghum GSS Repeats) Fruit fly (Repbase drorep)
  Wheat (TIGR Triticum GSS Repeats)
 
4
 
Submit to start the pipeline or Reset to start over.