[1] Family specific gene prediction software:

(1)tRNAscan-SE: Search for tRNA genes in genomic sequence. It identifies 99–100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. website: http://lowelab.ucsc.edu/tRNAscan-SE/

(2) snoScan: Search for guide box C/D box  snoRNA genes in a genomic sequence. website: http://lowelab.ucsc.edu/snoscan/.

(3) snoSeeker: Search for guide and orphan box C/D and H/ACA snoRNAs in a large genomic sequence or whole genome alignments(WGAs). snoSeeker has been used to scan four human–mammal whole-genome alignment (WGA) sequences and chicken-vertebrate WGA. website: http://genelab.sysu.edu.cn/snoSeeker/

(4) snoGPS: Search for H/ACA snoRNA genes in a genomic sequence. website:http://lowelab.ucsc.edu/snoGPS/

(5) snoReport: Computational identification of snoRNAs with unknown targets. website:http://www.bioinf.uni-leipzig.de/Software/snoReport

[2] noncoding gene prediction softwares:

(1)QRNA: QRNA uses comparative genome sequence analysis to detect conserved RNA secondary structures, including both ncRNA genes and cis-regulatory RNA structures. website: http://selab.janelia.org/software.html

(2)RNAz: Fast and reliable prediction of noncoding RNAs from multiple alignment sequences. It combine a measure for thermodynamic stability with a measure for structure conservation. RNAz has been successfully applied to many species.  website:http://www.tbi.univie.ac.at/~wash/RNAz/

(3)evoFold: EvoFold is a comparative method for identifying functional RNA structures in multiple-sequence alignments.  website: http://users.soe.ucsc.edu/~jsp/EvoFold/

[1] Family specific gene prediction software:

(1)tRNAscan-SE: Search for tRNA genes in genomic sequence. It identifies 99–100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. website: http://lowelab.ucsc.edu/tRNAscan-SE/

(2) snoScan: Search for guide box C/D box  snoRNA genes in a genomic sequence. website: http://lowelab.ucsc.edu/snoscan/.

(3) snoSeeker: Search for guide and orphan box C/D and H/ACA snoRNAs in a large genomic sequence or whole genome alignments(WGAs). snoSeeker has been used to scan four human–mammal whole-genome alignment (WGA) sequences and chicken-vertebrate WGA. website: http://genelab.sysu.edu.cn/snoSeeker/

(4) snoGPS: Search for H/ACA snoRNA genes in a genomic sequence. website:http://lowelab.ucsc.edu/snoGPS/

(5) snoReport: Computational identification of snoRNAs with unknown targets. website:http://www.bioinf.uni-leipzig.de/Software/snoReport

[2] noncoding gene prediction softwares:

(1)QRNA: QRNA uses comparative genome sequence analysis to detect conserved RNA secondary structures, including both ncRNA genes and cis-regulatory RNA structures. website: http://selab.janelia.org/software.html

(2)RNAz: Fast and reliable prediction of noncoding RNAs from multiple alignment sequences. It combine a measure for thermodynamic stability with a measure for structure conservation. RNAz has been successfully applied to many species.  website:http://www.tbi.univie.ac.at/~wash/RNAz/

(3)evoFold: EvoFold is a comparative method for identifying functional RNA structures in multiple-sequence alignments.  website: http://users.soe.ucsc.edu/~jsp/EvoFold/