Banana Slug Genomics

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
Created contig using these paired-end reads:
<code>
/campusdata/BME235/Spring2015Data/SW019_S2_L008_R1_001.fastq 
/campusdata/BME235/Spring2015Data/SW019_S2_L008_R2_001.fastq
</code>
Original contig sequence:
<code>
>variant-5304/0 4716
TCCACCGCCTTCGTCCAGTGGAGAATTCGTCGATTCAGAACAAGCCAAGAGAAGAAAGACAGATCCTCCTCCTACAACAT
CAACACCAGAGCCGGGTACAGGAACCAGACACGGACTACGTAGTGGAACACCTTTGGTTACTCCGGTTAAACCAAACACA
CCAGCAGCTCCAACAGCTGGGCCTAGTACCAGAACACCACAAAATACACCAGCCGGCTCACCAATGGCAGCATCAGTACC
GGCGGCAAACATGGACACCAGTGGTGCCCCAGGAGGTGATGTAATGCCAGCAGGAGAGGCAGATGCGGCTGGATATCCAG
TACCTGCAGGCATGGCAGGTTCAGGCGGTAATAGGTTTTTCACAGGATTTGGATCCCATACTCAAAAAGAACCAGATGGT
TACAGCTCAGTAACCAGGTCCTACAGCAAGACCTTTCTTGTGCACACCAACTTTGACGGCACTCTAAAAGCACTGATCAA
TATGGAACCTGGGGTCGCAGTACCAACAGGGATTACCAGTTCAGCAAAAGCAGAATGCATTGTGAACCATGGAGGGGTTA
TGATTCCATACATGTATCAAAATTGCTCTACAGACCCTTGGGACTGGAATGTGCCTGATCACTTCATGGGCTGGCAATGC
CAGGAGTATGGCTTTAAGGTGGCAGAAGCCCGCATAGAGACCCTAAACAATGACAAGCCCACACCAGAATCGGTGCCCGG
GCCACCGCCCCCTAGAGCCAGAATGTGGGCTTTTGTGGATGTTGACAACGATTATGGGCTGGATGACCACAGTGGGATCC
TCCAGCACAGTGACTTTTTCAGGGATCAAAATGCCCACAGCCCCAATGCCAATACGCAAGCTAAACTGCCTAACCAGCCA
GACAGAAAATTTTTACTGGACAAGCAAGCTGCACAGCAATCATTGTGCCAAGCCTTTACTAGAGCTTCTGGAGCAGGCAC
TGAGTCATTTGCTACTTATGAACCGAACTACGTGTGGGACATGTTCAAGTCAGATGGTTATGAAGAGTTTCAACTATGCG
ACGGTGACATGCAGCTGGTCTACAAATACAACGGTCCGGTACAACGTTTTCAACACAACCATGACTCCCTTGCACTAGAC
TGCTCAGGATTTACACCAGCCATGAACCTTCAAGATGATTTCTCCAACCTAGATGCTTTTGAGACTCAGCTTTGGCCAGG
AGCCAGAGAGCTACAAAGGCCATCAGGAACAGAGACCAGCGGTCAGCTAGGCATGATCAACTATGTCAACCACAATTTTG
TAAAGGACAGATTTAAAGTGGTGGATACTGACCCACTGTCCACAGTAGAACAGGACTACATAAACCAGACTGGGCAGATG
CCTCTAATAGCCAACATGGGCACCAATCACTTGGGCACTAGAACTGCTACTAATCCCAACATGTCAGATGATAACAAAAC
ATGGAAACAAACCTTCTCAAAAAGGCCCCCCATCTACATGTTTGGGGTTCACAAGGAGTGGGAATTTCAAACCACCGGTA
CACACCCTTACAGGTACTATTTTTGTGCACGGGTGACCTACCACAGCAAAGTCAAGTTTCTAATTAACCAAAGAGGGTGG
AAGCCAGTCATTCACGCAGGCTTTGGACTATATTCAGATTACAGCCCAATAAACAATCTTAACTGTGTATCCGTTCCAAG
GGCACAAGGAGAAGTTGCCCGCGCAAATAGACGTACCAAGGGCCACAAAATGATTGGCACAGGCAGATTTACCGCCAGTT
CTGGTCTATAAAAGCTCAGGGTAAGTAGAGTGCTAGTTATGTTCACTGCCGTTTTCAAGATGTTGAGGTCTTATTTAGCT
CGTGATGAAGTTAGGTACCACATGGTTACTGTGGGTCACTGTAGTAGACCAATTATTCACCCCTCATACTTTGTACCGAG
GGCTTTGGCCAAGGACAAGTCTGGAAATAAAGTTTCAGCATCAGCAGGTTATGACAAGAGCTACGAACTGGACCACTACT
CTGTCTATGAGGAACTGGTAGCAGTTTGGAACACTCCCAATGTTCACTTGGCGGCTATGGATGCCAAACACAAACAAGTG
ATCAATAACATTAAAGGCTTTACCAGAGATGAGAGATTCAAGGTGTTAATGGTGTTTCATGACAAGAGTTGTGCCAAACA
GTACAAGTCAAATGGCAATCACCTTCATTTGGTGATAAAGACATTAGTACCGGTAATGAGTTCTGACAACAAATATAGAG
CCATGATGAGAAGCATGAGCGGCATAGGTGGATACTGTAACACGGCTTTGCTAAAAGGTGACCGTTCATCTTTCCTGAGT
TACCTGGCTTCTGACCCTGAGAAAATGTTTCTAGGGTGTCAAGATGCTGACCTTCTACAAGAGTTTAAAGATGCTGAAAA
CTTTTCTGGTACGATTAAAGACTGGTTACTAGAAGATCAAAGTGACAAAACCAGTGCCATTAGAAGCTGGTCAGATGCCC
TGCCTGTGCCTTCAGATGTGCTCGTTCCTTGTGATTTAAATGTAGCCAGCACCAGCGATACACAGATCCCTAAACACATG
ACCAGTGAAAAGGCATCGGACACTGTGAAATTTCTATATGATGAACTGAAAAAGTTCCCTAATGCCCGGTCACTGACAGA
CCTCATGGGCATGTATGGGGGCTGGACCCCAGTCTGGAGTGCCTTATGTAATGTTGGGGCCACTCAGGCTGGTAAGAATG
CCTTTAACATGGCTTTACAAACAATACTGTTGGAGGCTAGCAAGATGACCCCACTAGCTACATGTGCAGAACTACAGGAT
TCTATTGTCGGCTACATGACCCCCAGGCATTCAGTAGCCATGTTGAACGCTTGGTGCATTGAACAGGGCATATCTCCTCG
CAAATGGTTTGCCTCTATGCACATGCTACTGTCCGGTAAAGGCAAAAAGAGAGTGGGAATTTATATGCAAGGTGAAGCCA
ATTCAGGAAAGACTATGATCACCAATTCCTGCTTTGATTGTTTGAATGACATTGTTGGAAAAATGACCAAAGATGGCTTC
CCCTTTCAACAACTTGGAAATAAGAGGATAGTTATTGGGGAAGAAGTGGCCATTACTACATCTAATTTGGAAAAGTTCAA
AGACCTCATGTCTGGTGGCAATGTGACCTGCGAGCGAAAGTGTACCACCCCACAGTATTGTAAGCCCAATTTGGTTCTGT
TGAACTCTAATGTAACCATCAAGGCTAACCTGTCTCAACATGAAGTGGTGATACTGAAAACCAGACTGTACCTGTTCGAA
AACCTGAAGCGATCAGCTGTTATCAACAGCTGTTACGGACTCATTCACCCCAAGGCATATGCCCTGTGTGAGGGCATTAC
CGATGATGATTACGCTGCCCTGATTTCCAATGAAACAGACCACTGGACAATGGACCCAGTTGAGATTCAAGGGTCCACTG
ATGTGTTTGAAGATGTTTGGGATACGATCCCAAAGGATTATGAGGGTCCACCCTTGACCCCCATTTGTAATCAAATGGAC
GTAGGGGAGATCCCCTGCTCACAGAAAAGATTTCGGCGTCGCCCATCTGATTTTGTTCATGAACCAGACTGGTTGCCTCA
TGATGAATCCTGGCATCCAGATATGGAGACCCCTGTTACCAAGGTTCGCAAGTTCTTGGACTACCCTGCTGAAGACCTTC
AGCACGATGAGCTTGTCCAGTCTGGTGATAAAGAGGTACAGTTTACAGATGAAGAAGTTTGTGATTTAATTGACTCTGAA
ATTGAAGATGCCCTGCATTCACACTGTGCCATTTTTGTTTCAGAACTAGAGACCTCTGGGAATCACATTTACCATGAACC
CATCGTCAACTTCAGAAGTGACGAGGACAGAGTCCCTTTCATTTCTAGATACGCCACGCTTTGGACAGCCGACCAGACTG
ATTTTATTCTTGAAGAAGTGGACGAATTCACTTCTGGTTTTGATAACGCTGACGTCCCTTGCCTTCACTACAGGAGTAGA
GCTCTCCCCCTTAACCAAAGGGGAACATTGCTTCAAGTTAACACCGTCAATGGCTCCATCACAAGACTGCTCGTCCCCCA
ATTGCCAGACTTTCAAGGACGCCAACCAAAGTGCTTCATTTTTCAAGAACGGAGAAAGACTGCTTGTCCCTTTTCCATTT
TGCCTCTGTACCCAGATGAATTCTACAGTGACAATACTTTTCTAATGATGTGCTACGCATATGTTATGCTGTGCACATAT
GAACTTACACACGTGTACCCAGATTCACCTACAGAATACCCAGAAAGTCAAGAAATGACCGACATTGTACTGCCCAAAGA
AGAAGATCCCATCAACACAAAGAACTGTTACTGGCAGGTCAGACAGAAGCTGAGACGCATCTTGGACGAAAAATATGTTG
ATGAATATGAACTTTCATTCAAAAAAGTTTGGTCTTTTACTAGATTTGCTTGCCATCTTTGGATCAGTAATGATTTTTAG
TGACATGACTTTTATATTTTCAGGATCCCTGACAGACAAAGACCATTAATATGCATTGCTTTTGTATTATTGTATTCTCA
GAATTTCATTCAATAAAGTCCTTACAAAGGACACACAAAACCAATGTCATGAATGGCTTGTCCTTTTCCTCTCTGAGCCT
TACAAGGCACCCTTTCTATACCTTTTGTGTGTGGGGGTAGGTCCTTTAAAGGGAAGGTACCACTTTTCCACATAAT
</code>
In this contig, I found this ORF
<code>
>variant-5304/0 4716|r0.611|2682|r0.611|894
MFTAVFKMLRSYLARDEVRYHMVTVGHCSRPIIHPSYFVPRALAKDKSGNKVSASAGYDKSYELDHYSVYEELVAVWNTPNVHLAAMDAKHKQVINNIKGFTRDERFKVLMVFHDKSCAKQYKSNGNHLHLVIKTLVPVMSSDNKYRAMMRSMSGIGGYCNTALLKGDRSSFLSYLASDPEKMFLGCQDADLLQEFKDAENFSGTIKDWLLEDQSDKTSAIRSWSDALPVPSDVLVPCDLNVASTSDTQIPKHMTSEKASDTVKFLYDELKKFPNARSLTDLMGMYGGWTPVWSALCNVGATQAGKNAFNMALQTILLEASKMTPLATCAELQDSIVGYMTPRHSVAMLNAWCIEQGISPRKWFASMHMLLSGKGKKRVGIYMQGEANSGKTMITNSCFDCLNDIVGKMTKDGFPFQQLGNKRIVIGEEVAITTSNLEKFKDLMSGGNVTCERKCTTPQYCKPNLVLLNSNVTIKANLSQHEVVILKTRLYLFENLKRSAVINSCYGLIHPKAYALCEGITDDDYAALISNETDHWTMDPVEIQGSTDVFEDVWDTIPKDYEGPPLTPICNQMDVGEIPCSQKRFRRRPSDFVHEPDWLPHDESWHPDMETPVTKVRKFLDYPAEDLQHDELVQSGDKEVQFTDEEVCDLIDSEIEDALHSHCAIFVSELETSGNHIYHEPIVNFRSDEDRVPFISRYATLWTADQTDFILEEVDEFTSGFDNADVPCLHYRSRALPLNQRGTLLQVNTVNGSITRLLVPQLPDFQGRQPKCFIFQERRKTACPFSILPLYPDEFYSDNTFLMMCYAYVMLCTYELTHVYPDSPTEYPESQEMTDIVLPKEEDPINTKNCYWQVRQKLRRILDEKYVDEYELSFKKVWSFTRFACHLWISNDF*
</code>
I ran this in BLASTp and it mapped to different parovirus NS1 proteins:
| Alignment | Max Score | Total Score | Query Coverage | e-value | Identity | Accession | 
|NS1 [Raccoon dog amdo ]|60.1|60.1|17%|7e-06|28%|AID57418.1|
|nonstructural protein [Turkey parvo  1078]|57.4|57.4|17%|6e-05|28%|ACA28962.1|
|NS1 [Chicken parvo ]|57.0|57.0|17%|7e-05|28%|AJB28744.1|

I chose to look at ACA28962.1.  Region 360:519 of my input sequence mapped with high probability this protein (the others as well).  The sequence for this is:
<code>
PRKWFASMHMLLSGKGKKRVGIYMQGEANSGKTMITNSCFDCLNDIVGKMTKDGFPFQQLGNKRIVIGEEVAITTSNLEKFKDLMSGGNVTCERKCTTPQYCKPNLVLLNSNVTIKANLSQHEVVILKTRLYLFENLKRSAVINSCYGLIHPKAYALCEG
</code>
I got the DNA from the contig at this part and it is:
<code>
>variant-5304/0 ACA28962.1|360:519aa|mult3original|extract
CGCAAATGGTTTGCCTCTATGCACATGCTACTGTCCGGTAAAGGCAAAAAGAGAGTGGGAATTTATATGCAAGGTGAAGCCAATTCAGGAAAGACTATGATCACCAATTCCTGCTTTGATTGTTTGAATGACATTGTTGGAAAAATGACCAAAGATGGCTTCCCCTTTCAACAACTTGGAAATAAGAGGATAGTTATTGGGGAAGAAGTGGCCATTACTACATCTAATTTGGAAAAGTTCAAAGACCTCATGTCTGGTGGCAATGTGACCTGCGAGCGAAAGTGTACCACCCCACAGTATTGTAAGCCCAATTTGGTTCTGTTGAACTCTAATGTAACCATCAAGGCTAACCTGTCTCAACATGAAGTGGTGATACTGAAAACCAGACTGTACCTGTTCGAAAACCTGAAGCGATCAGCTGTTATCAACAGCTGTTACGGACTCATTCACCCCAAGGCATATGCCCTGTGTGAGGGC
</code>
I just ran PriceTI with the following script:
<code>
/afs/cats.ucsc.edu/users/b/jolespin/PriceTI/PriceTI -fpp /campusdata/BME235/Spring2015Data/SW019_S2_L008_R1_001.fastq /campusdata/BME235/Spring2015Data/SW019_S2_L008_R2_001.fastq 100 95 -icf /campusdata/BME235/virus/virus_seed.fa 1 1 5 -nc 30 -dbmax 72 -mol 30 -tol 20 -mpi 80 -target 90 2 1 1 -o virus_assembly.fa -a 32
</code>
I'll update accordingly.
 
-jolespin
Banana Slug Genomics

User Tools

Site Tools

Page Tools
