Prodigal是为细菌和古菌基因组进行蛋白编码基因预测的软件。 可分析单基因组或宏基因组。 生成基因预测结果、基因核酸序列和蛋白序列。

基因组序列： fasta格式，例如 >seqname1 AAAAAAAAGCTACTTGGAGTACCAATAATAAAGTGAGCCCACCTTCCTGGTACCCAGACATTTC g: 指定翻译密码子 (default 11). p: 选择注释程序 (单基因组 or 宏基因组). Default is single.

基因gff文件 例如 ##gff-version 3 # Sequence Data: seqnum=1;seqlen=5129;seqhdr="scaffold4 61.7" # Model Data: version=Prodigal.v2.6.1;run_type=Single;model="Ab initio";gc_cont=71.11;transl_table=11;uses_sd=1 scaffold4 Prodigal_v2.6.1 CDS 2 4498 430.8 - 0 ID=1_1;partial=10;start_type=GTG;rbs_motif=GGAGG;rbs_spacer=5-10bp;gc_cont=0.697;conf=99.99;score=430.82;cscore=429.13;sscore=1.69;rscore=10.03;uscore=-5.18;tscore=-3.17; 基因核酸序列文件 基因氨基酸序列文件

tRNAscan-SE: An improved tool for transfer RNA detection tRNAscan-SE was written in the PERL (version 5) script language. Input consists of DNA or RNA sequences in FASTA format. tRNA predictions are output in standard tabular or ACeDB format. tRNAscan-SE does no tRNA detection itself, but instead combines the strengths of three independent tRNA prediction programs by negotiating the flow of information between them, performing a limited amount of post-processing, and outputting the results in one of several formats.

序列文件： fasta格式，例如 >seqname1 AAAAAAAAGCTACTTGGAGTACCAATAATAAAGTGAGCCCACCTTCCTGGTACCCAGACATTTC 类型: -E : search for eukaryotic tRNAs (default) -B : search for bacterial tRNAs -A : search for archaeal tRNAs -M <span><</span>model> : search for mitochondrial tRNAs options: mammal, vert -O : search for other organellar tRNAs

1. trna汇总表 out.gff 例如 Sequence tRNA Bounds tRNA Anti Intron Bounds Cove Name tRNA # Begin End Type Codon Begin End Score Note -------- ------ ----- ------ ---- ----- ----- ---- ------ ------ tig00000462_pilon_pilon 1 1742900 1742984 Leu GAG 0 0 57.02 tig00000462_pilon_pilon 2 2139254 2139329 Leu CAA 0 0 51.89 tig00000462_pilon_pilon 3 2955236 2955309 Gly TCC 0 0 81.79 tig00000462_pilon_pilon 4 3034584 3034656 Arg TCT 0 0 78.55 2. tRNA结构文件 out.tRNA.struc 例如 tig00000462_pilon_pilon.trna1 (1742900-1742984) Length: 85 bp Type: Leu Anticodon: GAG at 34-36 (1742933-1742935) Score: 57.02 * | * | * | * | * | * | * | * | Seq: GTCCGGGTGGCGGAATGGCaGACGCGCTAGCTTGAGGTGCTAGTGCCCTTTATCGGGCGTGGGGGTTCAAGTCCCCCCTCGGACA Str: >>>>>>>..>>>..........<span><</span><span><</span><span><</span>.>>>>>.......<span><</span><span><</span><span><</span><span><</span><span><</span>.>>>>......<span><</span><span><</span><span><</span><span><</span>..>>>>>.......<span><</span><span><</span><span><</span><span><</span><span><</span><span><</span><span><</span><span><</span><span><</span><span><</span><span><</span><span><</span>. 3. trna序列文件 trna.fasta 例如 >tig00000462_pilon_pilon.trna1 tig00000462_pilon_pilon:1742900-1742984 (+) Leu (GAG) 85 bp Sc: 57.02 GTCCGGGTGGCGGAATGGCAGACGCGCTAGCTTGAGGTGCTAGTGCCCTTTATCGGGCGT GGGGGTTCAAGTCCCCCCTCGGACA

使用barrnap软件对细菌、古细菌、线粒体、真核等做rna预测。 并使用脚本提取rna序列 If you use Barrnap in your work, please cite: Seemann T barrnap 0.9 : rapid ribosomal RNA prediction https://github.com/tseemann/barrnap

fasta:基因组序列文件 例如 >seqname1 AAAAAAAAGCTACTTGGAGTACCAATAATAAAGTGAGCCCACCTTCCTGGTACCCAGACATTTC kingdom : Kingdom: bac euk mito arc (default 'bac') lencutoff : Proportional length threshold to label as partial (default '0.8') reject : Proportional length threshold to reject prediction (default '0.25') evalue : Similarity e-value cut-off (default '1e-06')

1. rrna.gff 例如 ##gff-version 3 tig00000462_pilon_pilon barrnap:0.9 rRNA 585562 585672 2.7e-13 - . Name=5S_rRNA;product=5S ribosomal RNA tig00000462_pilon_pilon barrnap:0.9 rRNA 585767 588884 0 - . Name=23S_rRNA;product=23S ribosomal RNA tig00000462_pilon_pilon barrnap:0.9 rRNA 589164 590687 0 - . Name=16S_rRNA;product=16S ribosomal RNA 2. rna.fasta 例如 >tig00000462_pilon_pilon:585561-585672 GGCGGCGTCCTACTCTCCCACAGGGTCCCCCCTGCAGTACCATCGGCGCTGAAAGGCTTAGCT TCCGGGTTCGGAATGTAACCGGGCGTTTCCCTAACGCTATAACCACCG

RepeatMasker Developed by Arian Smit and Robert Hubley Please refer to: Smit, AFA, Hubley, R. & Green, P "RepeatMasker" at http://www.repeatmasker.org RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Sequence comparisons in RepeatMasker are performed by the program cross_match, an efficient implementation of the Smith-Waterman-Gotoh algorithm developed by Phil Green, or by WU-Blast developed by Warren Gish

fasta格式例如(可以是多条序列)： >seq1 AAAAAAAAGCTACTTGGAGTACCAATAATAAAGTGAGCCCACCTTCCTGGTACCCAGACATTTC

*.tbl 重复序列预测结果 *.masked 屏蔽掉重复序列的新序列 *.out 重复序列预测结果整理后的表格

**EggNOG-mapper** is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. The use of orthology predictions for functional annotation permits a higher precision than traditional homology searches (i.e. BLAST searches), as it avoids transferring annotations from close paralogs (duplicate genes with a higher chance of being involved in functional divergence). Benchmarks comparing different eggNOG-mapper options against BLAST and InterProScan [can be found here](https://github.com/jhcepas/emapper-benchmark/blob/master/benchmark_analysis.ipynb). EggNOG-mapper is also available as a public online resource: http://eggnog-mapper.embl.de # Documentation https://github.com/jhcepas/eggnog-mapper/wiki If you use this software, please cite: [1] eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Carlos P. Cantalapiedra, Ana Hernandez-Plaza, Ivica Letunic, Peer Bork, Jaime Huerta-Cepas. 2021. Molecular Biology and Evolution, msab293, https://doi.org/10.1093/molbev/msab293 [2] eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Jaime Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars J Jensen, Christian von Mering, Peer Bork Nucleic Acids Res. 2019 Jan 8; 47(Database issue): D309–D314. doi: 10.1093/nar/gky1085

基因的蛋白序列文件（fasta格式） 例如： >geneName1 MKLLAHILCLSLALAWAQSQDHALAVLDRCEGLEMDAVAVNEEGIPYFFKGDHLFKGFHG >geneName2 MWVGEERFEGSRLVVVTRGAVSVGGEGVEDVGGGAVWGLVRSAQSEHPGRFVLVDADVDA DVDTGVVPDVVGLGESQVAVRGGRVWVPRLVGVNSGGGVRAGGGVVRRGLGSGVALVTGG TGLLGGLVARHLVSAYGVGELVLVSRRGPGAPGVGALVGELEELGAGVRVVACDVADRGA VAELVGSIEGLRVVVHAAGAVDDGVIGSLDGGRLRGVMGPKAWGAWHLHELTSGLDLS

注释的结果表格文件 格式例如： #query seed_ortholog evalue score eggNOG_OGs max_annot_lvl COG_category Description Preferred_name GOs EC KEGG_ko KEGG_Pathway KEGG_Module KEGG_Reaction KEGG_rclass BRITE KEGG_TC CAZy BiGG_Reaction PFAMs geneName3 494419.ALPM01000100_gene1074 4.15e-05 48.9 COG0747@1|root,COG0747@2|Bacteria,2GM5G@201174|Actinobacteria 201174|Actinobacteria E ABC transporter substrate-binding protein - - - ko:K02035 ko02024,map02024 M00239 - - ko00000,ko 00001,ko00002,ko02000 3.A.1.5 - - SBP_bac_5