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Table 1 List of non-proprietary isomiR alignment programs

From: Evaluation of high-throughput isomiR identification tools: illuminating the early isomiRome of Tribolium castaneum

Program Usage Alignment method Publisher
isomiR-SEA 1.60 Command line
isomiR-SEA_1_6 -s tca -l 10 -b 4 -i < in_path > −p < out_path > −ss 6 -h 11 -m < mature_mir_file > −t < countfile>
User-defined seed size (default 6) Urgese et al. [21]
isomiRID 0.53 Command line
standard config file
bowtie1 de Oliveira et al. [22]
miraligner
3. Feb 2016
Command line
java -jar miraligner.jar -sub 1 -trim 3 -add 3 -s tca -freq
8 nt seed Pantano et al. [23]
IsomiRage Desktop GUI bowtie1 Muller et al. [24]
DeAnnIso Webapp bowtie1 and BLAST Zhang et al. [25]
isomiRex Webapp bowtie1 Sablok et al. [26]
miR-isomiRExp Webapp – offline bowtie1 Guo et al. [27]
  1. The three command line tools were used for our comparative evaluation. The others were discarded because they were incompatible with local high-throughput pipelines