Multi Rev Trans

Multi Rev Trans accepts a protein alignment and uses a codon usage table to generate a graph that can be used to find regions of minimal degeneracy at the nucleotide level. Each position in the resulting DNA sequence is shown as a group of four horizontal bars, each representing the probability that the position is occupied by a particular base. If one of the bars is longer than the "highlight" value you specify, the group of bars is highlighted. Use Multi Rev Trans to design PCR primers for amplifying genes that encode similar proteins.

Paste the protein alignment in FASTA or GDE format into the text area below.
>seq1 MGHSLILFGIQSDAYAFIPTTNEVVALCCSKEYAECCTES >seq2 ------MSFGYTETTLTKELIKDAAEK-CTRNRQECCIEI >seq3 MG--LILFGIQSDAYAFKETTNEAVALCCSKEYAECCTES

Highlight bases if their probability is at least

Enter the codon table you wish to use (in GCG format). The default codon usage table was generated using all the Caenorhabditis elegans coding sequences in GenBank. It was obtained from the Codon Usage Database.
AmAcid Codon Number /1000 Fraction .. Gly GGG 33645.00 4.42 0.08 Gly GGA 239815.00 31.51 0.59 Gly GGT 83309.00 10.94 0.21 Gly GGC 48904.00 6.42 0.12 Glu GAG 177583.00 23.33 0.37 Glu GAA 306826.00 40.31 0.63 Asp GAT 265858.00 34.93 0.68 Asp GAC 126840.00 16.66 0.32 Val GTG 106776.00 14.03 0.23 Val GTA 76084.00 10.00 0.16 Val GTT 185624.00 24.39 0.39 Val GTC 101576.00 13.34 0.22 Ala GCG 58775.00 7.72 0.13 Ala GCA 150062.00 19.71 0.32 Ala GCT 168695.00 22.16 0.36 Ala GCC 92562.00 12.16 0.20 Arg AGG 30055.00 3.95 0.08 Arg AGA 118910.00 15.62 0.30 Ser AGT 92683.00 12.18 0.15 Ser AGC 62102.00 8.16 0.10 Lys AAG 195352.00 25.66 0.40 Lys AAA 293866.00 38.61 0.60 Asn AAT 233637.00 30.69 0.62 Asn AAC 142124.00 18.67 0.38 Met ATG 198098.00 26.02 1.00 Ile ATA 76740.00 10.08 0.16 Ile ATT 250975.00 32.97 0.53 Ile ATC 144266.00 18.95 0.31 Thr ACG 64815.00 8.51 0.15 Thr ACA 152288.00 20.01 0.34 Thr ACT 146051.00 19.19 0.33 Thr ACC 79178.00 10.40 0.18 Trp TGG 84775.00 11.14 1.00 End TGA 10221.00 1.34 0.38 Cys TGT 88740.00 11.66 0.56 Cys TGC 70726.00 9.29 0.44 End TAG 4792.00 0.63 0.18 End TAA 12125.00 1.59 0.45 Tyr TAT 137130.00 18.02 0.56 Tyr TAC 106284.00 13.96 0.44 Leu TTG 154874.00 20.35 0.23 Leu TTA 80030.00 10.51 0.12 Phe TTT 192523.00 25.29 0.51 Phe TTC 185958.00 24.43 0.49 Ser TCG 87694.00 11.52 0.14 Ser TCA 156562.00 20.57 0.26 Ser TCT 130439.00 17.14 0.21 Ser TCC 80631.00 10.59 0.13 Arg CGG 33683.00 4.43 0.09 Arg CGA 87949.00 11.55 0.22 Arg CGT 84025.00 11.04 0.21 Arg CGC 38257.00 5.03 0.10 Gln CAG 103953.00 13.66 0.33 Gln CAA 206547.00 27.13 0.67 His CAT 107908.00 14.18 0.61 His CAC 69445.00 9.12 0.39 Leu CTG 89951.00 11.82 0.14 Leu CTA 61236.00 8.04 0.09 Leu CTT 163247.00 21.45 0.25 Leu CTC 111548.00 14.65 0.17 Pro CCG 68419.00 8.99 0.19 Pro CCA 196570.00 25.82 0.54 Pro CCT 68045.00 8.94 0.19 Pro CCC 33561.00 4.41 0.09

[home]