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blastn and phylogenetic tree


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#1 juanna

juanna

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Posted 28 May 2013 - 04:01 PM


Hi,


I just received the sequencing lists for my unknown bacterial. There are 5 unknown bacteria that I need to identify.

I would like to identify the bacteria using blastn and construct phylogenetic tree using neighbor joining.

Can anyone help me how to do it, since I not sure and familiar with it. Please help me as fast as possible.

Thanks.


Below are the lists of my sequencing results.



>1st_BASE_1215970_B_subtilis_168_Bacillus_Family_F.ab1

GGATTTCATATATTCGTCCTACAGCTAGCGTCATTGGAACTGGCATGTAAACTGGGATACCTCCGGGAAACCGGGGCTGA

TACCGGATGGTGGTTTAAACCGCATGGTTCAAACATAAAAGGTGGCTTCGGCTACCACTTACAGATGGACCCGCGGCGCA

TTAGCTAGTTGGTGAGGTAACGGCTCACCAAGGCAACGATGCGTAGCCGACCTGAGAGGGTGATCGGCCACACTGGGACT

GAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGC

GTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAGAACAAGTACCGTTCGAATAGGGCGGTACCTTGA

CGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATT

ATTGGGCGTAAAGGGCTCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAA

CTGGATA


>1st_BASE_1212247_TKM_2_Bacillus_Family_F.ab1

TGGAAGGGGGGTATTGGGAACTGGAGATTGCCGTGGGTAACTTGCCTGTAAGACTGGGATAACTCCGGGAAACCGGGGCT

AATACCGGATGCTTGTTTGAACCGCATGGTTCAAACATAAAAGGTGGCTTCGGCTACCACTTACAGATGGACCCGCGGCG

CATTAGTTAGTTGGTGAGGTAACGGCTCACCAAGGCAACGATGCGTAGCCGACCTGAGAGGGTGATCGGCCACACTGGGA

CTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCC

GCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAGAACAAGTACCGTTCGAATAGGGCGGTACCTT

GACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAA

TTATTGGGCGTAAAGGGCTCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGA

AACTGGATAA



>1st_BASE_1212249_TKM_6_Bacillus_Family_F.ab1
NGGGGGAACGGAGTAGGGGGGACGGAGAGTACACGTGGGTAACCTGCCTGTAAGACTGGGATAACTCCGGGAAACCGGGG
CTAATACCGGATGCTTGTTTGAACCGCATGGTTCAAACATAAAAGGTGGCTTCGGCTACCACTTACAGATGGACCCGCGG
CGCATTAGCTAGTTGGTGAGGTAACGGCTCACCAAGGCAACGATGCGTAGCCGACCTGAGAGGGTGATCGGCCACACTGG
GACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACG
CCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAGAACAAGTACCGTTCGAATAGGGCGGTACC
TTGACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGG
AATTATTGGGCGTAAAGGGCTCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTG
GAAACTGGAAAA


>1st_BASE_1214998_NL_3A_Bacillus_Family_F.ab1

TTTGGGGGGTGGGAGGGGGAACTGGAGCTAGCGCGTGGGTAACCTGCCTGTAAGACTGGGATACCTCCGGGAAACCGGGG

CTAATACCGGATGCTTGTTTGAACCGCATGGTTCAAACATAAAAGGTGGCTTCGGCTACCACTTACAGATGGACCCGCGG

CGCATTAGCTAGTTGGTGAGGTAACGGCTCACCAAGGCAACGATGCGTAGCCGACCTGAGAGGGTGATCGGCCACACTGG

GACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACG

CCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAGAACAAGTACCGTTCGAATAGGGCGGTACC

TTGACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGG

AATTATTGGGCGTAAAGGGCTCGCATGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTG

GAAACTGGATAA



>1st_BASE_1215001_CNL_2A_16S_532F2.ab1
NNNNNNNTNNNGACGTGAGCGNTACGCGNCNTGCTGACACANNCGTTTCTTGTGTNGATGCCCCCCCCGCAATNCCCTGG
GAGCTGCATCCAAAACTGGCGAGCTAGAGTACGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATAT
AGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACAGGA
TTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCAACTAGCCGTTGGAATCCTTGAGATTTTAGTGGCGCAGCTAACG
CATTAAGTTGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAG
CATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACAAN


#2 juanna

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Posted 28 May 2013 - 04:06 PM


Hi,


I just received the sequencing lists for my unknown bacterial. There are 5 unknown bacteria that I need to identify.

I would like to identify the bacteria using blastn and construct phylogenetic tree using neighbor joining.

Can anyone help me how to do it, since I not sure and familiar with it. Please help me as fast as possible.

Thanks.


Below are the lists of my sequencing results.



>1st_BASE_1215970_B_subtilis_168_Bacillus_Family_F.ab1

GGATTTCATATATTCGTCCTACAGCTAGCGTCATTGGAACTGGCATGTAAACTGGGATACCTCCGGGAAACCGGGGCTGA

TACCGGATGGTGGTTTAAACCGCATGGTTCAAACATAAAAGGTGGCTTCGGCTACCACTTACAGATGGACCCGCGGCGCA

TTAGCTAGTTGGTGAGGTAACGGCTCACCAAGGCAACGATGCGTAGCCGACCTGAGAGGGTGATCGGCCACACTGGGACT

GAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGC

GTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAGAACAAGTACCGTTCGAATAGGGCGGTACCTTGA

CGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATT

ATTGGGCGTAAAGGGCTCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAA

CTGGATA


>1st_BASE_1212247_TKM_2_Bacillus_Family_F.ab1

TGGAAGGGGGGTATTGGGAACTGGAGATTGCCGTGGGTAACTTGCCTGTAAGACTGGGATAACTCCGGGAAACCGGGGCT

AATACCGGATGCTTGTTTGAACCGCATGGTTCAAACATAAAAGGTGGCTTCGGCTACCACTTACAGATGGACCCGCGGCG

CATTAGTTAGTTGGTGAGGTAACGGCTCACCAAGGCAACGATGCGTAGCCGACCTGAGAGGGTGATCGGCCACACTGGGA

CTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCC

GCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAGAACAAGTACCGTTCGAATAGGGCGGTACCTT

GACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAA

TTATTGGGCGTAAAGGGCTCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGA

AACTGGATAA



>1st_BASE_1212249_TKM_6_Bacillus_Family_F.ab1
NGGGGGAACGGAGTAGGGGGGACGGAGAGTACACGTGGGTAACCTGCCTGTAAGACTGGGATAACTCCGGGAAACCGGGG
CTAATACCGGATGCTTGTTTGAACCGCATGGTTCAAACATAAAAGGTGGCTTCGGCTACCACTTACAGATGGACCCGCGG
CGCATTAGCTAGTTGGTGAGGTAACGGCTCACCAAGGCAACGATGCGTAGCCGACCTGAGAGGGTGATCGGCCACACTGG
GACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACG
CCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAGAACAAGTACCGTTCGAATAGGGCGGTACC
TTGACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGG
AATTATTGGGCGTAAAGGGCTCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTG
GAAACTGGAAAA


>1st_BASE_1214998_NL_3A_Bacillus_Family_F.ab1

TTTGGGGGGTGGGAGGGGGAACTGGAGCTAGCGCGTGGGTAACCTGCCTGTAAGACTGGGATACCTCCGGGAAACCGGGG

CTAATACCGGATGCTTGTTTGAACCGCATGGTTCAAACATAAAAGGTGGCTTCGGCTACCACTTACAGATGGACCCGCGG

CGCATTAGCTAGTTGGTGAGGTAACGGCTCACCAAGGCAACGATGCGTAGCCGACCTGAGAGGGTGATCGGCCACACTGG

GACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACG

CCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAGAACAAGTACCGTTCGAATAGGGCGGTACC

TTGACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGG

AATTATTGGGCGTAAAGGGCTCGCATGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTG

GAAACTGGATAA



>1st_BASE_1215001_CNL_2A_16S_532F2.ab1
NNNNNNNTNNNGACGTGAGCGNTACGCGNCNTGCTGACACANNCGTTTCTTGTGTNGATGCCCCCCCCGCAATNCCCTGG
GAGCTGCATCCAAAACTGGCGAGCTAGAGTACGGTAGAGGGTGGTGGAATTTCCTGTGTAGCGGTGAAATGCGTAGATAT
AGGAAGGAACACCAGTGGCGAAGGCGACCACCTGGACTGATACTGACACTGAGGTGCGAAAGCGTGGGGAGCAAACAGGA
TTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCAACTAGCCGTTGGAATCCTTGAGATTTTAGTGGCGCAGCTAACG
CATTAAGTTGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAG
CATGTGGTTTAATTCGAAGCAACGCGAAGAACCTTACAAN


#3 pito

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Posted 29 May 2013 - 09:39 AM

you can use this website: http://itol.embl.de/other_trees.shtml , to make trees.

read it carefully and then you should be able to make a tree yourelf.
You need some information of the bacteria (from the NCBI website), then you can load this data in the website and then you can produce the tree...

If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.





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