<div dir="ltr"><div><div>Hi,<br></div>I followed the protocol in given link <a href="http://khmer-protocols.readthedocs.org/en/latest/mrnaseq/6-annotating-transcript-families.html">http://khmer-protocols.readthedocs.org/en/latest/mrnaseq/6-annotating-transcript-families.html</a><br><br></div><div>After running this command<br></div><div><pre>annotate-seqs.py trinity-nematostella.renamed.fa nema.x.mouse.ortho nema.x.mouse.homol<br><br></pre><pre>I got following output as below, Also pasted the first few lines from each output file.<br><br>(khmerEnv)q@dx4-biotek12:~/Software/Annotation$ ./eel-pond-master/annotate-seqs.py trinity-nematostella.renamed.fa nema.x.mouse.ortho nema.x.mouse.homol <br>Scanning sequences -- first pass to gather info<br>... 0<br>... 25000<br>... 50000<br>... 75000<br>... 100000<br>... 125000<br>... 150000<br>... 175000<br>... 200000<br>second pass: annotating<br>... x2 0<br>... x2 25000<br>... x2 50000<br>... x2 75000<br>... x2 100000<br>... x2 125000<br>... x2 150000<br>... x2 175000<br>... x2 200000<br>----<br>207533 sequences total<br>0 annotated / ortho<br>0 annotated / homol<br>0 annotated / tr<br>0 total annotated<br><br>annotated sequences in FASTA format: trinity-nematostella.renamed.fa.annot<br>annotation spreadsheet in: trinity-nematostella.renamed.fa.annot.csv<br>annotation spreadsheet with sequences (warning: LARGE): trinity-nematostella.renamed.fa.annot.large.csv<br><br><b><br><br><br>less</b> <b>trinity-nematostella.renamed.fa.annot<br></b>&gt;nema.id1.tr89018 1_of_1_in_tr89018 len=261 id=1 tr=89018 <br>CAGCCTTTAGAAGGAAACAGTGGCAATATATAATTCTAGATGAAGCTCAGAATATCAAAAATTTTAAAAGTCAAAGGTGGCAGTTGCTGTTGAATTTTTCAAGTCAGAGGAGACTTTTGTTGACTGGAACACCTTTGCAGAACAATTTGATGGAGCTGTGGTCGCTTATGCATTTCCTCATGCCATCAATGTTTGCTTCTCATAAAGATTTTAGGGAGTGGTTTTCTAACCCTGTTACAGGGATGATTGAAGGGAATTCAG<br>&gt;nema.id2.tr459575 1_of_1_in_tr459575 len=217 id=2 tr=459575 <br>GCCAGTTGCAAACACGAATTTCAATCCATTAACATTTCATGAGTTGGAATCTCCACAGAAACTTTCTTTTCATCACGACCCCTGTTCCAAATGATTCCTTTCACACAAAACTGACCGGACAGGAAACAGAAAAAACAAGCAAGGGTCATGCAATAGACGACTTATTACCGGAAACCGCGATATTTAGCCAAGACATAAGTGCAAATTAAAACATCGA<br>&gt;nema.id3.tr219232 1_of_1_in_tr219232 len=252 id=3 tr=219232 <b><br><br><br><br>less trinity-nematostella.renamed.fa.annot.csv</b><br>sequence name,unique ID,Transcript family,ortholog,homology score,homolog,family orthology,family homology,additional information<br>nema.id1.tr89018 1_of_1_in_tr89018 len=261 id=1 tr=89018,id1,tr89018 1_of_1_in_tr89018 len=261 id=1 tr=89018,,,,,,<br>nema.id2.tr459575 1_of_1_in_tr459575 len=217 id=2 tr=459575,id2,tr459575 1_of_1_in_tr459575 len=217 id=2 tr=459575,,,,,,<br>nema.id3.tr219232 1_of_1_in_tr219232 len=252 id=3 tr=219232,id3,tr219232 1_of_1_in_tr219232 len=252 id=3 tr=219232,,,,,,<br>nema.id4.tr355712 1_of_1_in_tr355712 len=226 id=4 tr=355712,id4,tr355712 1_of_1_in_tr355712 len=226 id=4 tr=355712,,,,,,<br>nema.id5.tr222444 1_of_1_in_tr222444 len=252 id=5 tr=222444,id5,tr222444 1_of_1_in_tr222444 len=252 id=5 tr=222444,,,,,,<br><br><b>less trinity-nematostella.renamed.fa.annot.large.csv</b><br>sequence name,unique ID,Transcript family,ortholog,homology score,homolog,family orthology,family homology,additional information,sequence<br>nema.id1.tr89018 1_of_1_in_tr89018 len=261 id=1 tr=89018,id1,tr89018 1_of_1_in_tr89018 len=261 id=1 tr=89018,,,,,,,CAGCCTTTAGAAGGAAACAGTGGCAATATATAATTCTAGATGAAGCTCAGAATATCAAAAATTTTAAAAGTCAAAGGTGGCAGTTGCTGTTGAATTTTTCAAGTCAGAGGAGACTTTTGTTGACTGGAACACCTTTGCAGAACAATTTGATGGAGCTGTGGTCGCTTATGCATTTCCTCATGCCATCAATGTTTGCTTCTCATAAAGATTTTAGGGAGTGGTTTTCTAACCCTGTTACAGGGATGATTGAAGGGAATTCAG<br><br><br><br><br></pre><pre>Regards<br></pre><pre>Imran Khan<br>Research Scholar,<br>University of Porto<br></pre><pre><br></pre></div></div>