PlasmidLibraryTools
Here we have the Chodera Lab Plasmid Library. It includes a csv, which is a download of the google spreadsheet in 'upkeep', and some tools to help analyze sequencing data.
plasmid_sequences - contains sequences for full plasmids
scripts - currently has T7-Term-verify-sequence.ipynb which has an example rough analysis of sequencing data compared to uniprot sequence
sequencing data by clone - contains sequencing results by clone ID
This is the plasmid library:
TO DO: Separate out into different files, rather than sheets in same file. Currently not done, as the Plasmid Library is the only one with much in it.
Below is a checklist for what still needs to be done to Complete the Chodera Lab Plasmid Library with what we already have in the lab.
Once this is done, we will only need to make sure to update when new plasmids/primers/proteins are added.
Fill in 'full insert sequence' fields automagically from sequencing and uniprot files. Maybe too ambitious.
We should include instructions here for adding to the library:
In the words of @jchodera 'Is there something that already does this for us'.
This is kind of a two part question:
ipynb. @Lucelenie has also looked into whether quartzy is useful for this, and it doesn't seem to be.Other possible tools we can use:
Please feel free to post your opinions of these tools or links other tools you have found that can help us do this!
This may just be because I'm using an ipython notebook, but using the same procedure to align sequencing results to uniprot sequences (amino acid) uses too much memory and crashes the browser when trying to align sequencing results to plasmid sequences (nucleotide).
Others have experienced similar things:
https://www.reddit.com/r/bioinformatics/comments/2qilqi/pairwise2_running_out_of_memory_need_a_better/
biopython/biopython#297
I went ahead and just used ApE to align the sequences for which here is an example results:
Mon Aug 22, 2016 11:40 EDT
pet_his6_cterm_trx_tev_lic.seq from 1 to 5121
Alignment to
Cterm-Trx-T7-Term.seq from 1 to 473
Matches(|):309
Mismatches(#):15
Gaps( ):7
Unattempted(.):4793
* * * * * * * * * *
1 TTCTTGAAGACGAAAGGGCCTCGTGATACGCCTATTTTTATAGGTTAATGTCATGATAATAATGGTTTCTTAGACGTCAGGTGGCACTTTTCGGGGAAAT 100
....................................................................................................
1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1
* * * * * * * * * *
101 GTGCGCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCGCTCATGAGACAATAACCCTGATAAATGCTTCAATAACATTGAAAAA 200
....................................................................................................
1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1
* * * * * * * * * *
201 GGAAGAGTATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGTTTTTGCTCACCCAGAAACGCTGGTGAAAGT 300
....................................................................................................
1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1
* * * * * * * * * *
301 AAAAGATGCTGAAGATCAGTTGGGTGCACGAGTGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAACGTTTT 400
....................................................................................................
1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1
* * * * * * * * * *
401 CCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTGTTGACGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGA 500
....................................................................................................
1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1
* * * * * * * * * *
501 ATGACTTGGTTGAGTACTCACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCCATAACCATGAGTGATAACAC 600
....................................................................................................
1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1
* * * * * * * * * *
601 TGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAA 700
....................................................................................................
1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1
* * * * * * * * * *
701 CCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGCAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTA 800
....................................................................................................
1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1
* * * * * * * * * *
801 CTCTAGCTTCCCGGCAACAATTAATAGACTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGTTTATTGCTGA 900
....................................................................................................
1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~NNNNNNNNNNNNTNNNNNTTCNNGNTGGNTGGNTTATNGTNGAT 44
* * * *
* * * * * * * * * *
901 TAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGGCCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGT 1000
................................................................||||||||||||||||||||||||||||||||||||
45 GNNTCTGNATGNNGTGAGCCGGGCACCTCGCGGTATCGCCGCGATCCTGGATCCTTATGGAGTTCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGT 144
* * * * * * * * * *
* * * * * * * * * *
1001 CAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAACTGTCAGACCAAGTTTACTCATATATACTTT 1100
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
145 CAGGCAACTATGGATGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGGTAACTGTCAGACCAAGTTTACTCATATATACTTT 244
* * * * * * * * * *
* * * * * * * * * *
1101 AGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCA 1200
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||#|||||||||||||||||||||||||||||||||#
245 AGATTGATTTAAAACTTCATTTTTAATTTAAAAGGATCTAGGTGAAGATCCTTTTTGATAATCTCTTGACCAAAATCCCTTAACGTGAGTTTTCGTTCCT 344
* * * * * * * * * *
* * * * * * * * *
1201 CTGAGCGT-CAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTTTCTG--CGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTA 1297
||||#||| || ||||||||#|####||||||||||||||||||||||||||||||#|| | #||||#|###||#|||||||||||||||||.....
345 CTGANCGTCCA-ACCCCGTANANNNNATCAAAGGATCTTCTTGAGATCCTTTTTTTNTGNNC---NAATCNGAAACTAGCAAACAAAAAAACCAC----- 435
* * * * * * * * *
* * * * * * * * * *
1298 CCAGCGGTGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAAATACTGTCCTTCTAGTGT 1397
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
1398 AGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTC 1497
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
1498 GTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACG 1597
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
1598 ACCTACACCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCG 1697
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
1698 GAACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTG 1797
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
1798 ATGCTCGTCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCT 1897
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
1898 GCGTTATCCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCG 1997
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
1998 AGGAAGCGGAAGAGCGCCTGATGCGGTATTTTCTCCTTACGCATCTGTGCGGTATTTCACACCGCATATATGGTGCACTCTCAGTACAATCTGCTCTGAT 2097
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
2098 GCCGCATAGTTAAGCCAGTATACACTCCGCTATCGCTACGTGACTGGGTCATGGCTGCGCCCCGACACCCGCCAACACCCGCTGACGCGCCCTGACGGGC 2197
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
2198 TTGTCTGCTCCCGGCATCCGCTTACAGACAAGCTGTGACCGTCTCCGGGAGCTGCATGTGTCAGAGGTTTTCACCGTCATCACCGAAACGCGCGAGGCAG 2297
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
2298 CTGCGGTAAAGCTCATCAGCGTGGTCGTGAAGCGATTCACAGATGTCTGCCTGTTCATCCGCGTCCAGCTCGTTGAGTTTCTCCAGAAGCGTTAATGTCT 2397
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
2398 GGCTTCTGATAAAGCGGGCCATGTTAAGGGCGGTTTTTTCCTGTTTGGTCACTGATGCCTCCGTGTAAGGGGGATTTCTGTTCATGGGGGTAATGATACC 2497
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
2498 GATGAAACGAGAGAGGATGCTCACGATACGGGTTACTGATGATGAACATGCCCGGTTACTGGAACGTTGTGAGGGTAAACAACTGGCGGTATGGATGCGG 2597
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
2598 CGGGACCAGAGAAAAATCACTCAGGGTCAATGCCAGCGCTTCGTTAATACAGATGTAGGTGTTCCACAGGGTAGCCAGCAGCATCCTGCGATGCAGATCC 2697
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
2698 GGAACATAATGGTGCAGGGCGCTGACTTCCGCGTTTCCAGACTTTACGAAACACGGAAACCGAAGACCATTCATGTTGTTGCTCAGGTCGCAGACGTTTT 2797
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
2798 GCAGCAGCAGTCGCTTCACGTTCGCTCGCGTATCGGTGATTCATTCTGCTAACCAGTAAGGCAACCCCGCCAGCCTAGCCGGGTCCTCAACGACAGGAGC 2897
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
2898 ACGATCATGCGCACCCGTGGCCAGGACCCAACGCTGCCCGAGATGCGCCGCGTGCGGCTGCTGGAGATGGCGGACGCGATGGATATGTTCTGCCAAGGGT 2997
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
2998 TGGTTTGCGCATTCACAGTTCTCCGCAAGAATTGATTGGCTCCAATTCTTGGAGTGGTGAATCCGTTAGCGAGGTGCCGCCGGCTTCCATTCAGGTCGAG 3097
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
3098 GTGGCCCGGCTCCATGCACCGCGACGCAACGCGGGGAGGCAGACAAGGTATAGGGCGGCGCCTACAATCCATGCCAACCCGTTCCATGTGCTCGCCGAGG 3197
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
3198 CGGCATAAATCGCCGTGACGATCAGCGGTCCAGTGATCGAAGTTAGGCTGGTAAGAGCCGCGAGCGATCCTTGAAGCTGTCCCTGATGGTCGTCATCTAC 3297
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
3298 CTGCCTGGACAGCATGGCCTGCAACGCGGGCATCCCGATGCCGCCGGAAGCGAGAAGAATCATAATGGGGAAGGCCATCCAGCCTCGCGTCGCGAACGCC 3397
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
3398 AGCAAGACGTAGCCCAGCGCGTCGGCCGCCATGCCGGCGATAATGGCCTGCTTCTCGCCGAAACGTTTGGTGGCGGGACCAGTGACGAAGGCTTGAGCGA 3497
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
3498 GGGCGTGCAAGATTCCGAATACCGCAAGCGACAGGCCGATCATCGTCGCGCTCCAGCGAAAGCGGTCCTCGCCGAAAATGACCCAGAGCGCTGCCGGCAC 3597
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
3598 CTGTCCTACGAGTTGCATGATAAAGAAGACAGTCATAAGTGCGGCGACGATAGTCATGCCCCGCGCCCACCGGAAGGAGCTGACTGGGTTGAAGGCTCTC 3697
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
3698 AAGGGCATCGGTCGACGCTCTCCCTTATGCGACTCCTGCATTAGGAAGCAGCCCAGTAGTAGGTTGAGGCCGTTGAGCACCGCCGCCGCAAGGAATGGTG 3797
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
3798 CATGCAAGGAGATGGCGCCCAACAGTCCCCCGGCCACGGGGCCTGCCACCATACCCACGCCGAAACAAGCGCTCATGAGCCCGAAGTGGCGAGCCCGATC 3897
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
3898 TTCCCCATCGGTGATGTCGGCGATATAGGCGCCAGCAACCGCACCTGTGGCGCCGGTGATGCCGGCCACGATGCGTCCGGCGTAGAGGATCGAGATCTCG 3997
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
3998 ATCCCGCGAAATTAATACGACTCACTATAGGGAGACCACAACGGTTTCCCTCTAGTGCCGGCTCCGGAGAGCTCTTTAATTAAGCGGCCGCCCTGCAGGA 4097
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
4098 CTCGAGTTCTAGAAATAATTTTGTTTAACTTTAAGAAGGAGATATAGTTAACCTCTACTTCCAATCCGGCTCTAGCGGCTCTATGAGCGATAAAATTATT 4197
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
4198 CACCTGACTGACGACAGTTTTGACACGGATGTACTCAAAGCGGACGGGGCGATCCTCGTCGATTTCTGGGCAGAGTGGTGCGGTCCGTGCAAAATGATCG 4297
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
4298 CCCCGATTCTGGATGAAATCGCTGACGAATATCAGGGCAAACTGACCGTTGCAAAACTGAACATCGATCAAAACCCTGGCACTGCGCCGAAATATGGCAT 4397
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
4398 CCGTGGTATCCCGACTCTGCTGCTGTTCAAAAACGGTGAAGTGGCGGCAACCAAAGTGGGTGCACTGTCTAAAGGTCAGTTGAAAGAGTTCCTCGACGCT 4497
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
4498 AACCTGGCCGGCAGTAGCCACCATCACCATCACCATTAATAACCAACTCCATAAGGATCCGCGATCGCGGCGCGCCACCTGGTGGCCGGCCGGTACCACG 4597
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
4598 CGTGCGCGCTGATCCGGCTGCTAACAAAGCCCGAAAGGAAGCTGAGTTGGCTGCTGCCACCGCTGAGCAATAACTAGCATAACCCCTTGGGGCCTCTAAA 4697
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
4698 CGGGTCTTGAGGGGTTTTTTGCTGAAAGGAGGAACTATATCCGGACATCCACAGGACGGGTGTGGTCGCCATGATCGCGTAGTCGATAGTGGCTCCAAGT 4797
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
4798 AGCGAAGCGAGCAGGACTGGGCGGCGGCCAAAGCGGTCGGACAGTGCTCCGAGAACGGGTGCGCATAGAAATTGCATCAACGCATATAGCGCTAGCAGCA 4897
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
4898 CGCCATAGTGACTGGCGATGCTGTCGGAATGGACGACATCCCGCAAGAGGCCCGGCAGTACCGGCATAACCAAGCCTATGCCTACAGCATCCAGGGTGAC 4997
....................................................................................................
436 ---------------------------------------------------------------------------------------------------- 436
* * * * * * * * * *
4998 GGTGCCGAGGATGACGATGAGCGCATTGTTAGATTTCATACACGGTGCCTGACTGCGTTAGCAATTTAACTGTGATAAACTACCGCATTAAAGCTTATCG 5097
....................................................................................................
436 --------------------------------------------------------------------------------------NGCTAAANNNNTCG 449
*
* * *
5098 ATGATAAGCTGTCAAACATGAGAA 5121
........................
450 CNTGNNTGCNNGATCTGACCTNCC 473
* * *
The notebook that is crashing and the ApE alignment are both in the most recent PR (#7).
Sent Steve's plasmids (Plasmid ID 1-13) for sequencing, and it seems they're having some trouble.
Calling Genewiz, they offered to help us out with a few more sequencing reactions for free, but even these repeats weren't perfect.
The last set of these sequencing results have now been committed in the most recent pull request (#7).
We have a time limit of 5 work days during which we can continue to analyze these for free/without resending the samples.
For now I've just opened them in EditSeq and made a text file of the sequence.
In the current rough ipynb the frame is picked manually, we want to do this automatically!
Possible useful tools people have already made:
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