Quanto è utile/interessante questa discussione:
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PrincipessaEly
Nuovo Arrivato
Prov.: TO
Città: Torino
7 Messaggi |
 Inserito il - 05 aprile 2007 : 14:51:13
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 Ciao a tutti,
qualcuno potrebbe aiutarmi con lo studio della bioinformatica dicendomi che differenza c'è fra "known gene" e "consensus CDS"?
E già che ci siamo  , sapete anche dirmi quale sia il motivo biologico dell'esistenza dei blocchi di allineamento EST-genomico?
Grazie a tutti.
Ely
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aguffanti
Nuovo Arrivato
Città: milano
2 Messaggi |
 Inserito il - 05 aprile 2007 : 17:20:10
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Ciao Princess (bel nick...)
che differenza c'è fra "known gene" e "consensus CDS"?
I known gene sono, appunto, geni di 'alta qualita' ' generati dall'UCSC Genome Browser team secondo criteri precisi:
The UCSC Known Genes track shows known protein-coding genes based on protein data from SWISS-PROT, TrEMBL, and TrEMBL-NEW and their corresponding mRNAs from GenBank.
mRNA sequences were aligned against the human genome using blat. When a single mRNA aligned in multiple places, only alignments having at least 98% base identity with the genomic sequence were kept. This set of mRNA alignments was further reduced by keeping only those mRNAs referenced by a protein in SWISS-PROT, TrEMBL, or TrEMBL-NEW.
Among multiple mRNAs referenced by a single protein, the best mRNA was selected, based on a quality score derived from its length, the level of the match between its translation and the protein sequence, and its release date. The resulting mRNA and protein pairs were further filtered by removing short invalid entries and consolidating entries with identical CDS regions.
Finally, RefSeq entries derived from DNA sequences instead of mRNA sequences were added to produce the final data set shown in this track. Disease annotations were obtained from SWISS-PROT.
I CCDS sono un progetto simile dell'NCBI. L'obiettivo e'sempre lo stesso: un set di geni ad alta qualita'
The NCBI, Ensembl, and Sanger (Havana) annotation of human genome assembly 36 was analyzed to identify additional CDSs that are consistently annotated. Existing CCDS IDs were tracked based on re-identification of an identical match, or based on finding a partial match for CDS structures that the collaboration has either agreed to revise or is under consideration for a revision. Partial matches occur due to synchronization issues; collaborating members update annotation according to each inhouse schedule.
This update includes both the addition of >3900 new CCDS IDs, as well as a removal of >400 CCDS IDs representing CDS annotations that were removed through a collaboration agreement or were no longer found consistently in the new annotation datasets (unintended change). Unintended annotation changes are expected to occur in large-scale computational annotation pipelines given the very large volume of data processed by somewhat different methods.
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E già che ci siamo , sapete anche dirmi quale sia il motivo biologico dell'esistenza dei blocchi di allineamento EST-genomico?
don't despair --- l'allineamento di EST su un genomico anche al di fuori di un gene o nell'introne di un gene noto (in senso od antisenso...) indica la presenza di un trascritto. Sono moltissimi i trascritti 'anomali' nel genoma, diverse decine di migliaia ...
In bocca al lupo per l'esame, spero di averti aiutato
Alessandro
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Alessandro Guffanti – Bioinformatics, Nanotechnologies Group
Institute of Biomedical Technologies, CNR
c/o CISI - Via Fantoli, 16/15 – 20138 Milano, Italy
Ph.: +39-0250320918 Fax: +39-0250320919
Email: alessandro.guffanti@itb.cnr.it
http://www.centro-cisi.com/ http://www.itb.cnr.it/
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