Read-through Similarity Analysis

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'A computational method to predict genetically encoded rare amino acids in proteins', Chaudhuri and Yeates

Submit your entire read-through ORF (FASTA formatted DNA sequence, all UPPERCASE,
ATGC only, no header) with ONLY ONE in-frame stop codon (TAA/TAG/TGA).
The ORF should start with the start codon or any codon (3' to the start codon) in-frame with the start codon.

TTGGCAGGGACAAGTAGAATGCAATACCCTGCAACCGTAAGAATCGTAAG GCTCCCTTGTACCGGTAAATTCGATATTACCTACGCTTTAAGGGCTTTCC AAAAGGGAGCCGATGCGGTTATGGTTGTAGGGTGAAAGAAAGGAGAGTGT GCCTACGAAACAGGTAACTTAAAGGCTGAGGAGAGGGTTAGGTTCGCTAA ACAATTATTAGATGAATTAGGAATTGGCGGAGACAGAATTGACATGTTTT TCATGTCTGCCGCTGAGGCAGATAAATTCGTCTCCGCCGTTAATGAAATG ACTGCAAGAGTTGAAAAACTCGGACCTAACCCTCTCAAAGCTCAGTAAAG CCGGAGATTAAAGGGATGAGTTCTCTCGGGAACCCGTCAAGGGACCGAGA GAACAACCGCCCCATAAGTAAGGGGTTCTCCGGCATTGCAAAACTAATTT AAACTTTTTAGGGTGATTACCTTGGCAGTTAAGGTAGGGATGATACAAC

RSA analysis scheme uses BLAST for database homology search and
CLUSTALW for multiple sequence alignment.

Please note that if the alignment do not encompass either side of the stop codon in the BLAST output file, no Z-value shall be computed. CLUSTAL multiple sequence alignment requires a Z-value higher than 7. If you want any of the fixed input options to be changed, please email me.

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Interesting links:

• RECODE database http://recode.genetics.utah.edu/
• SECISSEARCH http://genome.unl.edu/SECISearch.html
  

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Maintained by Neel.
If you have any problem, please let me know.
 
Email: neel@mbi.ucla.edu