Table 1.
Bioinformatics scheme for identifying novel transcripts
| Steps in the scheme | Number of sequences | |
| Removed | Remaining | |
| Starting set of 5' placenta ESTs | 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 |
a NA; not applicable.