AphidBase Tutorial
1) Annotation of Acyrthosiphon pisum genome (in progress)
2) Annotation of Acyrthosiphon pisum ESTs on Drosophila melagogaster genome
3) Annotation of Acyrthosiphon pisum genomic contigs
1) A.pisum22801 genomic scaffolds as reference
2) D.melanogaster chromosomes as reference
This part has been constructed to compare D.
melanogaster chromosomes
with
A. gambiae cDNAs and A. pisum (the pea aphid) contigs.
Pea aphid contigs were formed
from the clusterization of about 60,000
ESTs (see Sabater-Munoz et al.
2006).
All the comparisons
were performed by a TBlastX.
This web site allows to:
1. Browse A. pisum contigs, A.
gambiae cDNAs and D. melanogaster chromosomes.
2. Access
the functionnal annotation of the A. pisum contigs.
| 1- Browse A. pisum sequences with hits on D. melanogaster |
| 2- Browse A. pisum sequences with NO hits on D. melanogaster |
These results are viewed with GBrowse,
a part of the wider
open source project GMOD.
GBrowse allows displaying sequences and annotations on genomes. In the following
figure,
are the explanation of the vizualisation of the Gbrowse page with links to others
pages.
Read also "gbrowse instructions" to help display your tips.
GBROWSE |
LINK |
 |
|
A. pisum CONTIG REPORT: link
description
 |
|
| List of all the A. pisum ESTs composing the contig. | |
| Consensus nucleotidic sequence of the contig. | |
| List of the cDNA libraries from which the ESTs composing the contig were isolated from. | |
| Amino acid sequences derived in the 6 frames from the nucleotic sequence of the contig. | |
| List of all the hits of the contig on the D. melanogaster chromosomes. | |
| List of the homologies of the contig with the sequences of the Uniprot database. | |
| Search for the longest open reading frame for the contig, using FrameD. | |
| Link
to the D. melanogaster litterature citing the gene homologous
to the A. pisum contig. |
|
| Link to a network of D. melanogaster genes which are co-cited with the gene homologous to the A. pisum contig. |
Blue cells: link available only for contigs
with hits.
A. pisum No hit CONTIG REPORT
When selecting "Sequences without hits" in home page, you may
choose a contig name
in a list or type/paste one.
You will be redirected to the same page than above (A. pisum CONTIG REPORT) but whitout bibliographic data and TblastX report.
3) A. pisum genomic
contigs as reference
In this part, the base rule represents the genomic contigs.
On the first track, gene predictions issued from the Gene_Id software
(
Parra et al. 2000 genome Research, vol 10 pp 511-515
)
are shown.
The other tracks below are the results of Blast analyses with:
>Uniprot.
>Drosophila melanogaster polypeptides.
>Apis mellifera peptides.
>Anopheles gambiae peptides.
>Acyrthosiphon pisum EST contigs.
>Acyrthosiphon pisum EST's.
For each feature, a url link is provided:
Gene-ID: local database
Uniprot hits: uniprot database
Drosophila melanogaster : flybase gene report
Apis mellifera : local database
Anopheles gambiae : Ensembl database
A. pisum EST contigs: EST contig reports from AphidBase
A. pisum ESTs: URGI database
|