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We construct an algorithm that generates large, band-diagonal transitionmatrices for a totally asymmetric exclusion process (TASEP) with local hoppingrate inhomogeneities. The matrices are diagonalized numerically to findsteady-state currents of TASEPs with local variations in hopping rate. Theresults are then used to investigate clustering of slow codons along mRNA.Ribosome density profiles near neighboring clusters of slow codons interact,enhancing suppression of ribosome throughput when such bottlenecks are closelyspaced. Increasing the slow codon cluster size, beyond $\approx 3-4$, does notsignificantly reduce ribosome current. Our results are verified by extensiveMonte-Carlo simulations and provide a biologically-motivated explanation forthe experimentally-observed clustering of low-usage codons

Clustered Bottlenecks in mRNA Translation and Protein Synthesis