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This article introduces the relevant knowledge of "how to install and use tRNAscanSE". In the operation of actual cases, many people will encounter such a dilemma, so let the editor lead you to learn how to deal with these situations. I hope you can read it carefully and be able to achieve something!

TRNA can be predicted using tRNAscanSE, which can identify more than 99% of tRNA genes with a sensitivity of less than 1 per 15m base false positives, and is currently the most powerful tool for predicting tRNA. TRNAscanSE can scan tRNA at the genome level. The software integrates three independent tRNA detection softwares, tRNAscan, EufindRNA and Cove, using perl. At run time, tRNAscan and EufindRNA are first called to identify the tRNA region in the genome sequence, and then Cove is called for verification.

The installation method is as follows:

Mkdir tRNAscantar-zxvf trnascan-se-2.0.5.tar.gzcd tRNAscan-SE-2.0./configure-- prefix= (path) / tRNAscan # the absolute path makemake installecho 'export PATH=$PATH: (path) / tRNAscan/bin' > > ~ / .bashrcsource ~ / .bashrc is omitted in parentheses. The tool depends on Infernal, and then install Infernal 1.1.2 The use of wget-c http://eddylab.org/software/infernal/infernal-1.1.2.tar.gzmkdir infernaltar-zxvf infernal-1.1.2.tar.gzcd infernal-1.1.2./configure-- prefix= (path) / infernalmakemake installecho 'export PATH=$PATH: (path) / infernal/bin' > > ~ / .bashrcsource ~ / .bashrctRNAscanSE is as follows: tRNAscan-SE-B-o tRNA.out-f rRNA.ss-m tRNA.stats genome.fasta-An is suitable for archaea. B is suitable for bacteria;-G is suitable for mixed sequences of archaea, bacteria and eukaryotes; and-O is suitable for mitochondria and chloroplasts. If the above options are not set, the default is suitable for eukaryotes;-C only uses Cove for tRNA analysis. Although the accuracy is improved to some extent, the running speed is very slow;-o result file name-f tRNA secondary structure result file name-m statistical result file name.

The bacterial genome sequence is predicted as follows:

TRNAscan-SE-B-o twk.tRNA.out-f twk.tRNA.ss-m twk.tRNA.stats new.scaffolds.fasta

The out file in the result file is the location and type information of the predicted tRNA on different Scaffolds:

The stats file is the predicted tRNA statistics, including the predicted number of tRNA, total bases, and so on, as follows:

The ss file is the tRNA secondary structure information, as follows:

The greater than sign or the less than sign indicates the complementary pairing region, and the dot sign indicates the annular region or the non-complementary pairing region. The sequence file and gff file of tRNA can be extracted from out file and genome sequence, as follows:

Perl 10_tRNAscan_parser.pl twk.tRNA.out new.scaffolds.fasta TWK

The results are as follows:

The sequence name is followed by the amino acids and anticodons carried by the tRNA. This is the end of the content of "how to install and use tRNAscanSE". Thank you for reading. If you want to know more about the industry, you can follow the website, the editor will output more high-quality practical articles for you!

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