annotation~Trinotate

add Trinotate annotation

input_1:Assembled cDNA contigs

input_1/Trinity.demo.fa

>TRINITY_DN2_c0_g1_i4 len=2218 path=[0:0-458 1:459-545 3:546-694 4:695-697 7:698-2217]
AGGGAATTCTCAGCAGCCGAGCATCTAGGAATATAGGAGGAGAGAGTTTACCTTGACTCTTTACATTTAGTCTGTCTATTTGATAAGGTTCCACTCAGCAGTGCGGTGAAGCGCCGGCGCAGACAGCCAAATTCACTTTTAGGGGATTGCGATAAGATTCTCTTCGGATTTCTCCAACAGGGTCCATTCCGCTTGAAGGGAGGCGAATTTATTCTTAAGTTTTAGACACTTTTATTCTGTGCTTCGTCTTTTTAGTTAGAACACAAATTTTTCAAAATGGCTGAGCGTATGAAACCAATGGGGATGGACCGTGCACTTTCGTCAAAGATGGGCGCTAAATATGACCCTGCTGCTGAGGCGGAAGTCAGGAACTGGATAAAACAGCTGATCGGCGAGGACATCGGTGACGGCGCCATGAACGTGGAGAAAAACCTCAGAGATGGAGTCATTCTTATCAAACTTTTACAAAAACTATACGAAGGGACCTCCAACCTACCCAACAAGGCCAGAACCATGAAACTCTCATACAACACAATGAATGCTCCTTTCAAACAGATGGAGAATATAGAAGTTTTCCTTAAAGGTGCAAACGCCTATGGTGTCCCCCTTAACAGTTTGTTCCAGACAGTTGACCTGTATGAAGGCAGAAATATGGCCATGGTCGTAGCCACTATTCTACAGCTGGGTACTGAGGCTCAAAGGAACGGTCATGAGTCGGTTGAAAAGGGCTTAATCTGTGGGGCAAAACCTGTCGAGAAACATGTGGTACATTTTACCGAGGAACAAAAGAGGGCAGGTCAAGGCATCATCGGATTACAAGCTGGAACAAACAAATGCGCAAGTCAAAAAGGAATGAAAATAGGAGGAGCACGCCACATTGCCGACATCAAAGCAGACGACATGAATCGTGAGGGCCAAGGTATACTTTCTGCTCAAGCAGGCACCAATAAATTTGCTTCCCAGAAGGGCATGTCGATCGGATCAGTCAGGCATATCGCTGACATTAGGGCAGACGACATGTCTCAAGAAGGTCACGGGGTCATTGGTCTACAAGCCGGAAGTAATAAGTTTGCAAGTCAATCGGGGATGAGTTTTGGCGCCGTTCGTCACATTTCGGACATAAGAGCTGACGACATGTCACAAGAAGGTCATGGGGTGATTGGTCTCCAGGCCGGAAGTAACAAGGGCGCAAGTCAATCGGGAATGAGTTTCGGTGCCGTTCGTCACATTTCGGACATTAGGGCCGATGATATGTCACAAGAAGGTCAAGGAGTTATTGGACTTCAGTCTGGAAGTAATCAATTTGCCAGTCAAAAGGGAATGTCGTTTGGAAACGTGCGTCATATTTCAGATATAAGAGCAGACGAAATGTCACAGGAAGGACAAGGAGTTATTGGCCTTCAATCCGGAAGTAACAAGGGCGCAAGTCAATCCGGAATGTCATTCGGAAGTGTTCGCCATATTGCCGATATCCGCGCGGATGAATACGACCAAAGCAGCGCCGGAACCATTGGACTGCAGTACGGCAGTAACGAAGGAGCGAGTCAATCAGGCATGACTGGATTCGGAACAACGCGCGGTGTGGCTGACATGAAAATTGACGATCTCGCCGAAGCTTCCAGGGCGATGTATTGAAGTGATTACAATGTATGATATGGGTTATAAGGACGAAAAGTACCAAAATCGACTTTGCTTTATCCAATGTTCGTGGTGTAATGAAAGACAGATCTGAGGCAATTTAGTAATATTTTTGAAAGGTAGTTACAATAACAAAAATACCGGTAAGACAGAGAAAACAAAAATGGAAATCAAAGAAATCATATATAGATTTCACAAGACGCATCATTAGACACATGTGTTAAAATTTTGAAAATAACAACAACAAAAATATTTAAGTGTAAATGAATATTATTCGGATTCTTCAAAAACTCTTATCTTTCTTTTTTCAAGGCGTCAATTTTCATGATGTCAACATTTCATTCCAAAATTTCTTTCATTTCACATCATTTCACTTGAATGTCTTGTTACGTTGGAATCATATATTAACGTGTTTTATGTAAAGTGTTTCTAGATTACTTACTTAGCTGCTTAACTTGTTGAAAATATCAGCTGTAAAGAAAATATACAACAGGCGATTAAAAAAATTGAAGTTTTAAGTGGAAAATATCGATCCTCGAGAGTTGAGTTAAGTAAATATTTTTGATTTACAGAAAGACAC
>TRINITY_DN2_c0_g1_i5 len=1851 path=[0:0-458 1:459-545 3:546-694 4:695-697 6:698-1424 8:1425-1539 10:1540-1850]
AGGGAATTCTCAGCAGCCGAGCATCTAGGAATATAGGAGGAGAGAGTTTACCTTGACTCTTTACATTTAGTCTGTCTATTTGATAAGGTTCCACTCAGCAGTGCGGTGAAGCGCCGGCGCAGACAGCCAAATTCACTTTTAGGGGATTGCGATAAGATTCTCTTCGGATTTCTCCAACAGGGTCCATTCCGCTTGAAGGGAGGCGAATTTATTCTTAAGTTTTAGACACTTTTATTCTGTGCTTCGTCTTTTTAGTTAGAACACAAATTTTTCAAAATGGCTGAGCGTATGAAACCAATGGGGATGGACCGTGCACTTTCGTCAAAGATGGGCGCTAAATATGACCCTGCTGCTGAGGCGGAAGTCAGGAACTGGATAAAACAGCTGATCGGCGAGGACATCGGTGACGGCGCCATGAACGTGGAGAAAAACCTCAGAGATGGAGTCATTCTTATCAAACTTTTACAAAAACTATACGAAGGGACCTCCAACCTACCCAACAAGGCCAGAACCATGAAACTCTCATACAACACAATGAATGCTCCTTTCAAACAGATGGAGAATATAGAAGTTTTCCTTAAA

input_2:gene2isoform map file

Option

-c '8' -m '64' 'input_1/Trinity.demo.fa'

Output

Trinotate.output.txt

transcript_id	#gene_id	sprot_Top_BLASTX_hit	RNAMMER	prot_id	prot_coords	sprot_Top_BLASTP_hit	Pfam	SignalP	TmHMM	eggnog	Kegg	gene_ontology_blast	gene_ontology_pfam	transcript	peptide	KEGG ORTHOLOGY ID	KEGG ORTHOLOGY NAME	KEGG MODULE NAME	KEGG PATHWAY NAME	NCBI NT top hit	e-value	similarity	hit length
TRINITY_DN2_c0_g1_i4	TRINITY_DN2_c0_g1_i4	CNN3_RAT^CNN3_RAT^Q:301-1125,H:11-271^38.71%ID^E:1.27e-42^RecName: Full=Calponin-3;^Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus`CNN3_RAT^CNN3_RAT^Q:1264-1596,H:160-271^44.915%ID^E:1.38e-14^RecName: Full=Calponin-3;^Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus`CNN3_RAT^CNN3_RAT^Q:1030-1359,H:160-271^44.248%ID^E:1.85e-13^RecName: Full=Calponin-3;^Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus`CNN3_RAT^CNN3_RAT^Q:1381-1599,H:160-233^48.649%ID^E:7.88e-11^RecName: Full=Calponin-3;^Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus	.	TRINITY_DN2_c0_g1_i4.p1	277-1635[+]	CNN3_RAT^CNN3_RAT^Q:9-283,H:11-271^38.71%ID^E:2.17e-44^RecName: Full=Calponin-3;^Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus`CNN3_RAT^CNN3_RAT^Q:330-440,H:160-271^44.915%ID^E:7.44e-15^RecName: Full=Calponin-3;^Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus`CNN3_RAT^CNN3_RAT^Q:252-361,H:160-271^44.248%ID^E:9.73e-14^RecName: Full=Calponin-3;^Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus`CNN3_RAT^CNN3_RAT^Q:369-441,H:160-233^49.351%ID^E:3.94e-11^RecName: Full=Calponin-3;^Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus	PF00307.31^CH^Calponin homology (CH) domain^26-141^E:6e-20`PF00402.18^Calponin^Calponin family repeat^178-201^E:1.9e-12`PF00402.18^Calponin^Calponin family repeat^217-240^E:1.1e-11`PF00402.18^Calponin^Calponin family repeat^256-279^E:5.7e-14`PF00402.18^Calponin^Calponin family repeat^295-318^E:8.8e-14`PF00402.18^Calponin^Calponin family repeat^334-357^E:1.5e-12`PF00402.18^Calponin^Calponin family repeat^373-396^E:1.7e-12`PF00402.18^Calponin^Calponin family repeat^412-434^E:8.3e-11	.	.	COG5199^Calponin	KEGG:rno:54321	GO:0005884^cellular_component^actin filament`GO:0005829^cellular_compone

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