Description
This track displays the alignment of California Condor (Gymnogyps
californianus) transcripts (sequenced using 454 high-throughput DNA
sequencing) to the chicken genome.
Methods
- The Condor read sequences were obtained from the NCBI
Trace Archives:
CENTER_NAME=WUGSC, CENTER_PROJECT=U_FC-MATT_TECHD2. The mean read size
is 110 bases.
- The Condor reads were aligned to a set of predicted transcript
sequences, then the read was projected to transcript alignments on the
genome using the predicted transcript alignments. This process improves
alignments across splice sites.
- Build a set of predicted transcripts sequences using PASA cluster
of chicken mRNA and EST BLAT alignments and N-SCAN gene predictions.
- Align Condor reads to transcripts using LASTZ.
- Project alignments onto the chicken genome.
- Filter alignments to remove duplicate alignments and small
fragments, keeping those that score within one percent of the
best alignment for a given read.
- Align reads that could not be mapped via the predicted transcript
directly to the chicken genome using LASTZ, and filter using the above
criteria.
After performing the above steps, the resulting number of sequences and
alignments of those sequences are summarized in this table:
| sequences | alignments |
454 reads | 419,240 | |
projected | 139,392 | 146,325 |
direct | 87,870 | 89,812 |
combined | 227,262 | 236,137 |
Credits
References
454 Sequencing:
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ,
Chen Z et al.
Genome sequencing in microfabricated high-density picolitre reactors.
Nature. 2005 Sep 15;437(7057):376-80.
PMID: 16056220; PMC: PMC1464427
BLASTZ/LASTZ:
Chiaromonte F, Yap VB, Miller W.
Scoring pairwise genomic sequence alignments.
Pac Symp Biocomput. 2002:115-26.
PMID: 11928468
Condor Sequencing:
Romanov MN, Tuttle EM, Houck ML, Modi WS, Chemnick LG, Korody ML, Mork EM, Otten CA, Renner T, Jones
KC et al.
The value of avian genomics to the conservation of wildlife.
BMC Genomics. 2009 Jul 14;10 Suppl 2:S10.
PMID: 19607652; PMC: PMC2966331
N-SCAN:
Gross SS, Brent MR.
Using multiple alignments to improve gene prediction.
J Comput Biol. 2006 Mar;13(2):379-93.
PMID: 16597247
PASA:
Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, Hannick LI, Maiti R, Ronning CM,
Rusch DB, Town CD et al.
Improving the Arabidopsis genome annotation using maximal transcript
alignment assemblies.
Nucleic Acids Res. 2003 Oct 1;31(19):5654-66.
PMID: 14500829; PMC: PMC206470
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