S288c Genome Chip

 

Unique YJM789 Sequences on the tiling chip

Sequences from YJM789 Genome Sequencing

Ted Jones identified sequences unique to strain YJM789 when compared to S288c during his assembly of the YJM789 shotgun sequence. These sequences are tiled on the S288c tiling chip. There are 85 individual sequences. To make it easier to analyze and view data from these sequences, I have arranged them in a single file. This allows for easier use of GTRANS and IGB. The individual sequences are separated by a string of"n's" in the sequence. I have called this the "faux_yjm" sequence. The order of the 85 individual sequences does not represent their true order in the YJM789 genome. I made a accompanying .gff file, that annotates the sequences. Here are links to download the chrfaux_yjm.fa sequence, the faux_yjm.gff annotation data, the 85 individual sequences in traditional multi-fasta format, and the location on the tiling chip of the Unique YJM789 probes in SGTC1lq format.

 

The sequences prepared by Ted were run through repeatmasker using yeast repetitive sequences before making Oligos for the chip. The masked sequences are represented by "Ns" in these files. The types of unique YJM789 sequences that are on the tiling chip are:

 

1. unique insertions in contigs that align with S288c sequence. These oligos have yjm789_ins in their name. 5282 bp in 53 different sequences, 4537 bp after masking.

2. end of contigs, unique sequence at the end yjm789 contig that aligns with S288c sequence. These oligos have yjm789-mend in their name. 9174 bp in 11 different sequences, 5818 bp after masking.

3. unmapped and no blast match. yjm789 contig that does not map to S288c sequence and does not have a S288c blast match. These oligos have yjm789-unloc in their names. 13764 bp in 21 different sequences, 10037 after masking.