annotation~blast

add blast annotation

input_1:query (FASTA file)

input_1/Bomo_gene_models.withnote.plus.NC_002355.gff3.with-geneid.genes.fasta

>KWMTBOMO02910 transcript=KWMTBOMO02910.mrna1
TGAATGAAGAAAAATTGTCTTTGCCGGCATCTTTAAATTCTTTCAAACTTGATTTACATTTCTCGGCGCCAAACGAACACCTGCTAAGTGATGCCGATGAATTTTGGCCAGCGGACATTGTATCTCCTACATTAAAACCAAGCGCAAGTGTCTGTAAATCCATTACATCTCTCGGTAAAATAATGGAATTCGAAGAACAAAGTTTACTCACAAGCGATCCTTCAGAAGAAAATTTGGAACATAAAGTCACAGAGGGGGAACAAACTTTCAGTATTTCACCTAAATCAGAGTTACCCACGAAAACTGGTCATATATTTAACGTAAACACCTTAAGCGACAGTTTCCCAAGATTAATAAGACAATTTGTGAATTTAGAGTATGGTGTTAACGAACAACTTGATACTGAAACAAATCACGACAATAAAATGGATAAGGCTCTTGATGAAAAAGATAATAATGTGGGAATTGGTAGTGAGTTTCAAAAATCACTCGATCCAACATCTAATGTGACCGCTACATTAGAGGATATAAGAGATTTAAAAAAAACAAGTGAAATAGAAAACGACATAAATGAAGTAAAAAAAAACATTGATAACGTACCTTTTGTAGATCTAAATATCGAATCAAAAAATATTACGAATGTGGTAAATATAGCACAAAATAATGTCCATTACCACCACGGAGAACGAACAAATATAAAAAGAGAATTTGATATTAAAACGTGGTGCACGGAATTGGAGCAGGGATATAAGAATTTGGAATTATGGAATTTATGGATTTCAAATGCATGTGAAGCAGTCCTACAAATTAAAAAAATAGAAGATTCGATAAGACTCTGCCCTATAAGAAGTCAGCAATATTGGAGAAATCTCAAAGCAAATATTGACAAAGATGCAACTATGTGGCTAAAGTTTAACAAACAAATACAAAACAAAGCTTATCTAATGAGTAACAACAATAAAAAGGTAGACAGATATCACTTGTTAAACAGGTACAAATTATAAATACCGGTTAACGTGAAATTTAATTTTCCAGAGGGTATTAAAAACAAATTGCAAAT
>KWMTBOMO01130 transcript=KWMTBOMO01130.mrna1
CTTTCATTTTTTTTTATTTCTCGTTAATTTACACCATTAGAAATTAATAACATAACAAAGGATTGTTTGGTAAAAAGTCGAAATGATTGGAGATTTAGCAGATTTCGACGATGTCAGCGACGTGATTTTAATACCACCAAAAAAGGGGATAAAGAATCATGCACTTGACTCATTAAGCATGATAGTCTTAGATGATGACGTTGGACATCCAAGTACCAGACAAACCTGTGACATAAAATATGATAAAATATTTTTAGACAATAAGAATTTAGTAAAATTTATAGAAAAATGTTTTGCTCTGGAGAATTCAGATGGGATGGCGAGAATTGTTAATCGCACATTATTAGGCTTGTACCAGAACACATGTCCTGAGTACAAAAGTTCACATCGGTTTCAAAATATTTTGGACAATGCCTTTATGAAGTTAGAGTTAGATCCAAAACACAAGTTCTCGCACATAAAAGGTGTGTGTGATGCATTGAAACTTCATAAAGTTAAGAAGAAGGCCAAGCTTATAACAATGTCCACAGCTTTACAAGATAAGTTAAAAGAAGACACTGCTCTTCAGAGAAGATCACCAGTAGATGGGGTTTCAAAAAAGAAATCTAGGTTTAACTTTATAAACTTAGATGATAATGGAGCAAACATTATAGAAATCAAAGATGATGACAGCGATGTAATTGTTGTTGACAACAGTTCAAAACTTTCAAATGAAAACAAAATCACTATAAGAGAAACAATTAAGACTGAAAATAGTACAAATGAACCTATGAAGGAAATGGATGTTGAAACGAAAATAATTAAGGATGTTCAAGATATTAATGTTGATTTTTTTATTATGAAAGATTCAGAAAGCAAGAAGACTGAACTGCTAGTACCTGTAGGAAAAAAATCCTCTACAATTGATACTGAGACTCGAATCAAGGAAATTGAAATTACTATTGCTAATTATAAAGAGAAAATAGTTAAGTTGGAGCAACAGGACGTTTGTGATGATTCTCTTTATTCACCATATATTCAGAGTGAAAAGTTAAAACAAAAGATTGTGGATCTGTATAAAGAGCTGTGTAGTCTTACTGGAGATGAGCCAATTAAAAGACGCGAAGTTCGACTGCAAGTTGCAAAAGATCATCCTCCTGCACCTGTACAAAAACTTGAACAGTTCCTCAATGAGAACATAGGGTCAAATGGAGAGCCACCGTTCCCTGATTTCCATGACGTGATGATGTGTGTAGCAGAGGCCAATGCTACTGAGAGTTTGGGCTGGAATGCTGTGCAGGTCATGTCTGAAGCAAATGCATTGTTCACTCAATGTGGTCGCGCTCTGCAAAAACGTCGTCAGCAACGCGAATGGCGAGACTTGCTATGTCGAGTCAGGAGCGAAGACTTGCGAGATCCTGCTGATGATGATCCCGAGCTGCTGGCAAGACTCGAGGAGAACCGACGCACGGCCGCAAAGAAGGAACGGGATCTTATGGAGAGGTTTACAAATATTGATTGCGACGTTCCCGGCCTTAACTTACATGTAGATATTAATGATTCGCACGATCAGATAGTGGACAAAAGCGACGAACAAGACAGCGACAGTGAGAAGGAGGAGAAAATTCCGATCTTCACTAATAAGGAAGTCAAAATAGAGAAAGACATTGAAACAGATAAACTCGACAGCTCCGACATTGAAACTAAAAAACTTGACAGTTCCAACAGTGACAACAATGAGGTCACTGCCGATGTCAAAGTAAAGATTGAACCCGTAGACCTATCAGTCCTTTACGAGTGTGTCGAGAACAGCGTTACATCAGTCATATTCGACGTCGAAGATCCATTTTTGGTGATTGAAATTTCGT

input_2:database (FASTA file)

input_2/dmel-all-translation-r6.29.fasta

>FBpp0070000 type=protein; loc=X:join(19963955..19964071,19964782..19964944,19965006..19965126,19965197..19965511,19965577..19966071,19966183..19967012,19967081..19967223,19967284..19967460); ID=FBpp0070000; name=Nep3-PA; parent=FBgn0031081,FBtr0070000; dbxref=FlyBase:FBpp0070000,FlyBase_Annotation_IDs:CG9565-PA,GB_protein:AAF45370.2,REFSEQ:NP_523417,GB_protein:AAF45370,UniProt/Swiss-Prot:Q9W5Y0,FlyMine:FBpp0070000,modMine:FBpp0070000; MD5=19dfee3c4d8ec74f121a5b5f7f7682e1; length=786; release=r6.29; species=Dmel; 
MTRYKQTEFTEDDSSSIGGIQLNEATGHTGMQIRYHTARATWNWRSRNKTEKWLLITTFVMAITIFTLLIVLFTDGGSSD
ATKHVLHVQPHQKDCPSGNELPCLNKHCIFASSEILKSIDVTVDPCDDFYGYSCNQWIKNNPIPEGKSTWGTFGKLEQMN
QLIIRNVLEKPAKSFKSDAERKAKVYYESCLDADEHMEKLGAKPMNDLLLQIGGWNVTKSGYNVANWTMGHTLKILHNKY
NFNCLFGWAIGEDDKNSSRHVIQIDQGGLTLPTADYYNNKTDNHRKVLNEYIEYMTKVCVLLGANESDARAQMIGVINFE
KKLANITIPLEDRRNEEAMYHPMQLRQLSKLAPFLNWTDHFDNAMQMVGRRVTDDEVVVVYAPDFLKNLSDIILKMEQTE
EGKITLNNYLVWQAVRTLTSCLSKPFRDAYKGVRKALMGSDGGEEIWRYCVSDTNNVVGFAVGAIFVRQAFHGESKPAAE
QMIAEIREAFKMNLQNLTWVDKQTREKAIEKANQISDMIGFPDYILDPVELDKKYAELNITPNAYFENNIQVAIYNLKSN
LKRLDQPVNKTNWGMTPQTVNAYYTPTKNQIVFPAGILQTPFFDINNPKSLNFGAMGVVMGHELTHAFDDQGREYDKFGN
INRWWDSKSIERFNEKSECIARQYSGYKMNGRTLNGKQTLGENIADNGGLKAAYHAYQRTKSDRDVDILKLPGLNLTHSQ

input_3:Gene expression file to be annotated (optional)

input_3/result.DESeq2.isoforms.count_table.Br.Fatbody.txt.Br.up.Fatbody.down.txt

Geneid	SRR4425244_1.fastq.bam (CPM)	SRR4425245_1.fastq.bam (CPM)	SRR4425248_1.fastq.bam (CPM)	SRR4425249_1.fastq.bam (CPM)	SRR4425250_1.fastq.bam (CPM)	SRR4425251_1.fastq.bam (CPM)	padj
rna-NC_002355_1_7618__8992	954.517	344.636	143.373	123.86	39126	38594.9	4.29053730778421e-41
KWMTBOMO15034	0	14.9842	26.0678	61.9302	24905.6	20171.5	1.23699026204414e-27
KWMTBOMO00091	136.36	194.794	156.407	111.474	9808.09	10293.8	7.96671716783547e-19
KWMTBOMO03805	0	0	0	0	16240.5	17147.1	4.4100050020729e-13
KWMTBOMO04904	0	0	0	0	5289.46	5216.28	1.874648181155e-09
KWMTBOMO11870	15.1511	29.9684	26.0678	12.386	2897.24	3856.72	6.05448440491857e-09
KWMTBOMO00396	30.3021	0	39.1017	12.386	2604.86	2247.44	1.31955796464941e-07
KWMTBOMO12781	45.4532	224.763	0	12.386	5342.62	5188.54	2.03322507191383e-07
KWMTBOMO15314	60.6042	104.889	26.0678	24.7721	1887.19	2635.89	2.95956992057532e-07

Option

-c "8" -m "64" -p "blastx" -d "" -b "-outfmt 6"

Output

result.DESeq2.isoforms.count_table.Br.Fatbody.txt.Br.up.Fatbody.down.txt.blastx.txt

Geneid	SRR4425244_1.fastq.bam (CPM)	SRR4425245_1.fastq.bam (CPM)	SRR4425248_1.fastq.bam (CPM)	SRR4425249_1.fastq.bam (CPM)	SRR4425250_1.fastq.bam (CPM)	SRR4425251_1.fastq.bam (CPM)	padj	Top Hit (dmel-all-translation-r6.29.fasta.Bomo_gene_models.withnote.plus.NC_002355.gff3.with-geneid.genes.fasta.blastx)	e-value
rna-NC_002355_1_7618__8992	954.517	344.636	143.373	123.86	39126	38594.9	4.29053730778421e-41		
KWMTBOMO15034	0	14.9842	26.0678	61.9302	24905.6	20171.5	1.23699026204414e-27	FBpp0310390 type=protein; loc=2L:complement(join(1361641..1361657,1361458..1361578,1360796..1360926,1360657..1360736,1360492..1360590,1360147..1360373)); ID=FBpp0310390; name=NLaz-PC; parent=FBgn0053126,FBtr0343844; dbxref=GB_protein:AHN54075,REFSEQ:NP_001285560,FlyBase:FBpp0310390,FlyBase_Annotation_IDs:CG33126-PC,UniProt/TrEMBL:Q8SXR1; MD5=172fd2123cff45e6c71f3b09fa170fa7; length=224; release=r6.29; species=Dmel; 	4.39e-15
KWMTBOMO00091	136.36	194.794	156.407	111.474	9808.09	10293.8	7.96671716783547e-19	FBpp0076722 type=protein; loc=3L:complement(join(6217594..6217815,6217103..6217249,6215095..6215719,6214802..6215011,6214329..6214742,6213990..6214262,6213071..6213923,6212364..6213015,6212021..6212301,6211726..6211954,6211198..6211668,6209236..6211136,6205977..6209168,6205693..6205907,6204175..6205628)); ID=FBpp0076722; name=LanA-PA; parent=FBgn0002526,FBtr0077014; dbxref=FlyBase:FBpp0076722,FlyBase_Annotation_IDs:CG10236-PA,GB_protein:AAF50672.2,REFSEQ:NP_476617,GB_protein:AAF50672,UniProt/Swiss-Prot:Q00174,FlyMine:FBpp0076722,modMine:FBpp0076722; MD5=9ed104ae31d2c7bd47b2a83fb50d21ea; length=3712; release=r6.29; species=Dmel; 	0.0
KWMTBOMO03805	0	0	0	0	16240.5	17147.1	4.4100050020729e-13	FBpp0309474 type=protein; loc=2R:join(19712397..19712450,19712510..19712851); ID=FBpp0309474; name=Obp56e-PB; parent=FBgn0034471,FBtr0340600; dbxref=GB_protein:AHN56415,REFSEQ:NP_001286620,FlyBase:FBpp0309474,FlyBase_Annotation_IDs:CG8462-PB,UniProt/TrEMBL:A0A0B4LFW3; MD5=53e300a0f87fff19fb1328fda5472469; length=131; release=r6.29; species=Dmel; 	2.28e-08
KWMTBOMO04904	0	0	0	0	5289.46	5216.28	1.874648181155e-09	FBpp0110455 type=protein; loc=3L:complement(join(23986264..23986308,23974598..23974660,23934880..23935121,23934555..23934825,23934415..23934494,23912278..23912455,23890061..23890206,23889860..23890010,23889105..23889799,23874248..23874431,23873992..23874188,23873610..23873924,23839922..23840180)); ID=FBpp0110455; name=CG40470-PA; parent=FBgn0058470,FBtr0111152; dbxref=FlyBase_Annotation_IDs:CG40470-PA,GB_protein:EAA46083.1,FlyBase:FBpp0110455,REFSEQ:NP_001036635,GB_protein:EAA46083,UniProt/TrEMBL:Q7PLV6,FlyMine:FBpp0110455,modMine:FBpp0110455; MD5=77a5aa45fda257e54b4fb120da28c27b; length=941; release=r6.29; species=Dmel; 	0.0
KWMTBOMO11870	15.1511	29.9684	26.0678	12.386	2897.24	3856.72	6.05448440491857e-09	FBpp0086747 type=protein; loc=2R:complement(join(13907589..13908218,13905222..13905501,13904248..13905161,13903814..13904182,13902654..13903572,13901687..13902317,13901437..

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