[BiO BB] cDNA annotation

[guoqing lu]

Dear group,

We have a big dataset from microarray experiments and
want to have them annotated. Annotation is expected to
be done following these steps:
1. Data pre-processing ( mask repeats and cloning
vector fragments). 
2. Database searches ( to examine whether the sequence
has a known protein, whether it has been localized,
and whether there is a possibility of forming a
contig).
3. EST clustering (initial clustering: performed based
on a measure of high sequence identity;  assembly;
alignment processing: get rid of errors and alternate
forms of expressed sequences;  Cluster joining) 
4. Finding an ORF
5. Find global homologies and align with sequence
6. Location and transmembrane segments
7. Motifs prediction
8. Structure prediction
 
Could you please give some comments? And does anybody
know any automatic annotation tools available online
or for download?

I appreciate your help!

Gabriel



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