Difference between revisions of "Texas Xenopus Genome Project/Species Identification"
From Marcotte Lab
| Line 34: | Line 34: | ||
</pre> | </pre> | ||
| − | * Run MUSCLE (version 4.0, with default option) for multiple sequence alignment. | + | * Run MUSCLE (version 4.0, with default option) for multiple sequence alignment. Interestingly, sequence from CHORI-216 is somewhat different, compared to both XENTR_mRNA and CHORI-219 fragment. |
<pre> $ mus4 -i XENTR_CHORI.fasta -o XENTR_CHORI.muscle </pre> | <pre> $ mus4 -i XENTR_CHORI.fasta -o XENTR_CHORI.muscle </pre> | ||
<pre> | <pre> | ||
| Line 66: | Line 66: | ||
XENTR_CH216-2E23 277 + c---------------aaatc 282(341) | XENTR_CH216-2E23 277 + c---------------aaatc 282(341) | ||
****************....* | ****************....* | ||
| + | </pre> | ||
| + | |||
| + | * Run MUSCLE again, only with XENTR_mRNA and CHORI-219 sequence. | ||
| + | <pre> | ||
| + | XENLA_CH219-20I1 1 + ttatttgtgccctggatacccctggaactatagcagggtgactgttaccccaatgtttctatat 64 | ||
| + | XENTR_NM_0011422 1 + ttatttgtgccctgggtacccctggaactatagcggggtgactgttaccccaatgtttctatat 64 | ||
| + | *************** ****************** ***************************** | ||
| + | |||
| + | XENLA_CH219-20I1 65 + atctgtaaccttgttattagctaagggggcccagtctgaaggtcagttagggggagatttgggg 128 | ||
| + | XENTR_NM_0011422 65 + atctgtaaccttgttatgggctaagggggcccagcctgaaggccagttagggggggatttgggg 128 | ||
| + | ***************** *************** ******* *********** ********* | ||
| + | |||
| + | XENLA_CH219-20I1 129 + tgagggcttatttgtaccctgggtacccctggaactatagcagggtgactgttaccccaatgtt 192 | ||
| + | XENTR_NM_0011422 129 + tgagtgcttatttgtgccctgggtacccctggaactatagcagggtgactgttaccccaatgtt 192 | ||
| + | **** ********** ************************************************ | ||
| + | |||
| + | XENLA_CH219-20I1 193 + tctatatatctgtaaccttgttatgagctaagggggcccagtctgaaggccagttagggggaga 256 | ||
| + | XENTR_NM_0011422 193 + tctatatatctgtaaccttgttatgggctaagggggcccagcctgaaggccagttaggggggga 256 | ||
| + | ************************* *************** ******************* ** | ||
| + | |||
| + | XENLA_CH219-20I1 257 + tatggggtgagtgtttatttgtgccctggttacccctggaactatagcagggtgac 312(1) | ||
| + | XENTR_NM_0011422 257 + tttggggtgagtgcttatttgtgccctgggtacccctggaactatagcagggtgac 312(1) | ||
| + | * *********** *************** ************************** | ||
</pre> | </pre> | ||
---- | ---- | ||
[[Category:XenopusGenome]] | [[Category:XenopusGenome]] | ||
Revision as of 11:12, 9 December 2009
Selection procedure
- Download X. tropicalis mRNA sequences from XenBase (Nov. 27, 2009 version).
- xdata:ID/XENTR_mRNA.xenbase20091127.fasta.gz 17 MB, gzipped.
- Download CHORI-216 sequences (from XenBase) and CHORI-219 sequences (from NCBI GenBank).
- xdata:ID/XENTR_CH216.fasta.gz 1.2 MB, gzipped. (CHORI-216 sequences. 160 BAC sequences from X. tropicalis genome)
- xdata:ID/XENLA_CH219.fasta.gz 6.5 MB, gzipped. (CHORI-219 sequences. 29 BAC sequences from X. laeves genome)
- Run BLAT (version 3.4, with default option) to known CHORI BAC sequences.
- xdata:ID/XENTR_mRNA.XENLA_CH219.blat_pslx.gz 1.2 MB, gzipped.
- xdata:XENTR_mRNA.XENTR_CH216.blat_pslx.gz 20 MB, gzipped.
blat XENTR_CH216.fasta XENTR_mRNA.xenbase20091127.fasta XENTR_mRNA.XENTR_CH216.blat_pslx -out=pslx
- Parse two BLAT output files with the following criteria.
- From X. tropicalis mRNA, only RefSeq (starts sith 'NM_') sequences are considered.
- Select X. tropicalis mRNA sequences which hit both CHORI-219 and CHORI-216 (minimum match length is 200 bp to be called as a 'hit'). For CHORI-219 hits, I only consider 10 BACs which we already knew that they are available ('74I8','204L9','197E3','71P23','36I4','35I18','262A22','20I13','206K7','166K18').
- Survey each hit blocks. If the same mRNA fragment hits both CHORI-219 and CHORI-216, report three sequences: the query sequence from X. tropicalis mRNA, the target sequence from CHORI-219 BACs (X. laevis) and the target sequence from CHORI-216 BACs (X. tropicalis). ONE hit block is reported.
>XENTR_NM_001142220_0 gi|213983084|ref|NM_001142220| ttatttgtgccctgggtacccctggaactatagcggggtgactgttaccccaatgtttctatatatctgtaaccttgttatgggctaaggggg cccagcctgaaggccagttagggggggatttggggtgagtgcttatttgtgccctgggtacccctggaactatagcagggtgactgttacccc aatgtttctatatatctgtaaccttgttatgggctaagggggcccagcctgaaggccagttagggggggatttggggtgagtgcttatttgtg ccctgggtacccctggaactatagcagggtgac >XENTR_CH216-2E23_0 tcaccccaaatccccccctaactggccttcaggctgggcccccttagctcataacaaggttacagatatatagaaacattggggtaacagtca ccccgctatagttccaggggtacccagggcacaaataagcactcaccccaaatcatcccctaactggccttcaggctgggcccccttagccca taacaaggttacagatatatagaaacattggggtaacagtcaccccgctatagttccaggggtacccagggcacaaataagcactcaccccaa atc >XENLA_CH219-20I13_0 ttatttgtgccctggatacccctggaactatagcagggtgactgttaccccaatgtttctatatatctgtaaccttgttattagctaaggggg cccagtctgaaggtcagttagggggagatttggggtgagggcttatttgtaccctgggtacccctggaactatagcagggtgactgttacccc aatgtttctatatatctgtaaccttgttatgagctaagggggcccagtctgaaggccagttagggggagatatggggtgagtgtttatttgtg ccctggttacccctggaactatagcagggtgac
- Run MUSCLE (version 4.0, with default option) for multiple sequence alignment. Interestingly, sequence from CHORI-216 is somewhat different, compared to both XENTR_mRNA and CHORI-219 fragment.
$ mus4 -i XENTR_CHORI.fasta -o XENTR_CHORI.muscle
XENLA_CH219-20I1 1 + ttattt----------------------gtgccctggatacccctggaactatagcagggtgac 42
XENTR_NM_0011422 1 + ttattt----------------------gtgccctgggtacccctggaactatagcggggtgac 42
XENTR_CH216-2E23 1 + tcaccccaaatccccccctaactggccttcaggctgggcccccttag-ctcataacaaggttac 63
*.*... .....****...***.*.**...***.*..***.**
XENLA_CH219-20I1 43 + tgttaccccaatgtttctatatatctgtaaccttgttattagct-aagggggcccagtctgaag 105
XENTR_NM_0011422 43 + tgttaccccaatgtttctatatatctgtaaccttgttatgggct-aagggggcccagcctgaag 105
XENTR_CH216-2E23 64 + agatatatagaaacattggggtaacagtcaccccgctatagttccaggggtacccagggc---- 123
.*.**.....*....*.....**.*.**.***..*.*** .... *.***..***** ..****
XENLA_CH219-20I1 106 + gtcagttagggggagatttggggtgagggcttatttg-----taccctgggtacccctggaact 164
XENTR_NM_0011422 106 + gccagttagggggggatttggggtgagtgcttatttg-----tgccctgggtacccctggaact 164
XENTR_CH216-2E23 124 + -acaaataagcactcaccccaaatcatcccctaactggccttcaggctgggcccc-cttagccc 185
* **..**.*... .*.......*.*. .*.**..** ....*****..*****....*.
XENLA_CH219-20I1 165 + atagcagggtgactgttaccccaatgtttctatatatctgtaaccttgttatgagctaa-gggg 227
XENTR_NM_0011422 165 + atagcagggtgactgttaccccaatgtttctatatatctgtaaccttgttatgggctaa-gggg 227
XENTR_CH216-2E23 186 + ataacaaggttacagatatatagaaacattggggtaacagtcaccccgctatagttccaggggt 249
***.**.***.**.*.**.....*....*.....**.*.**.***..*.***......* ***.
XENLA_CH219-20I1 228 + gcccagtctgaaggccagttagggggagatatggggtgagtgtttatttgtgccctggttaccc 291
XENTR_NM_0011422 228 + gcccagcctgaaggccagttagggggggatttggggtgagtgcttatttgtgccctgggtaccc 291
XENTR_CH216-2E23 250 + acccagggca---------------caaataagcact----------------------caccc 276
.***** ...***************...**..*...****** *************** .****
XENLA_CH219-20I1 292 + ctggaactatagcagggtgac 312(341)
XENTR_NM_0011422 292 + ctggaactatagcagggtgac 312(341)
XENTR_CH216-2E23 277 + c---------------aaatc 282(341)
****************....*
- Run MUSCLE again, only with XENTR_mRNA and CHORI-219 sequence.
XENLA_CH219-20I1 1 + ttatttgtgccctggatacccctggaactatagcagggtgactgttaccccaatgtttctatat 64
XENTR_NM_0011422 1 + ttatttgtgccctgggtacccctggaactatagcggggtgactgttaccccaatgtttctatat 64
*************** ****************** *****************************
XENLA_CH219-20I1 65 + atctgtaaccttgttattagctaagggggcccagtctgaaggtcagttagggggagatttgggg 128
XENTR_NM_0011422 65 + atctgtaaccttgttatgggctaagggggcccagcctgaaggccagttagggggggatttgggg 128
***************** *************** ******* *********** *********
XENLA_CH219-20I1 129 + tgagggcttatttgtaccctgggtacccctggaactatagcagggtgactgttaccccaatgtt 192
XENTR_NM_0011422 129 + tgagtgcttatttgtgccctgggtacccctggaactatagcagggtgactgttaccccaatgtt 192
**** ********** ************************************************
XENLA_CH219-20I1 193 + tctatatatctgtaaccttgttatgagctaagggggcccagtctgaaggccagttagggggaga 256
XENTR_NM_0011422 193 + tctatatatctgtaaccttgttatgggctaagggggcccagcctgaaggccagttaggggggga 256
************************* *************** ******************* **
XENLA_CH219-20I1 257 + tatggggtgagtgtttatttgtgccctggttacccctggaactatagcagggtgac 312(1)
XENTR_NM_0011422 257 + tttggggtgagtgcttatttgtgccctgggtacccctggaactatagcagggtgac 312(1)
* *********** *************** **************************
