## 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

- Sample collection and analysis was done by Michael Romanov and Oliver Ryder of the San Diego Zoo's Institute for Conservation Research and Elaina Tuttle and Rusty Gonser of the Dept. of Biology, Indiana State University.
- 454 sequencing and analysis was done by Matthew T Hickenbotham, Jarret Glasscock, Sean McGrath and Elaine R Mardis:

          Washington University Genome Sequencing Center
          Washington University School of Medicine
          Campus Box 8501
          4444 Forest Park Ave.
          St. Louis, MO 63108

- PASA clusters and N-SCAN gene predictions were provided by Jeltje van Baren of the Brent Lab at Washington University Saint Louis.
- Alignments and tracks were produced by Mark Diekhans of the UCSC Genome Bioinformatics group.

## 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.

### BLASTZ/LASTZ:

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002;:115-26.

### 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.

### N-SCAN:

Gross SS, Brent MR. Using multiple alignments to improve gene prediction. In Proc. 9th Int'l Conf. on Research in Computational Molecular Biology (RECOMB '05):374-388 and J Comput Biol. 2006 Mar;13(2):379-93.

### PASA:

Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith Jr RK, 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.