Table 1 Bioinformatics scheme for identifying novel transcripts
From: Discovery and characterization of 91 novel transcripts expressed in cattle placenta
Steps in the scheme | Number of sequences | |
|---|---|---|
| Â | Removed | Remaining |
Starting set of 5' placenta ESTs | Â | 12,614 |
PipeBLASTN (automated BLASTN analysis) | 10,235 | 2,379 |
In silico extension of 5' ESTs with public cattle ESTs, followed by PipeBLASTN | 581 | 1,798 |
3' reads from single-pass sequencing using anchored oligodT primer | 618 | 1,180 |
PipeBLASTN of 3' reads | 404 | 776 |
Assembly of 3' and extended 5' mates | NAa | 493 |
Full-clone sequencing of unassembled 3' ESTs | NA | 283 |
In silico extension of 493 mate-pairs followed by PipeBLASTN | 171 | 322 |
In silico extension of 283 primer-walked clones, followed by PipeBLASTN | 232 | 51 |
Working set of divergent homologs and novel transcripts (322+51) | NA | 373 |
TBLASTX against UniGene databases to separate novel transcripts from divergent homologs | 75 | 298 |
In silico extension followed by PipeBLASTN using updated databases to yield final set of NTs. | 134 | 164 |
Screening for internal poly A tracts | 73 | 91 |