Exercises/Project2/Primer_pairs.txt

-Name	Primer1	Primer2
-M01	22	23
-M02	26	27
-M03	30	31
-M05	42	43
-M06	46	47
-M07	NT12	NT13
-M09	130	131
-M11	NT10	NT11
-M12	206	207
-M13	03_NT04	03_NT05
-M14	03_NT22	03_NT23
-M15	03_NT26	03_NT27
-M16	03_NT56	03_NT57
-M20	424	425
-M21	426	427
-M22	430	431
-M23	NT18	NT19
-M24	NT34	NT35
-M25	504	505
-M26	606	607
-M27	622	623
-M29	628	629
-M30	704	705
-M31	708	709
-M32	710	711
-M33	712	713
-M34	800	801
-M36	NT16	NT17
-M37	900	901
-M38	1000	1001
-M39	1002	1003
-M41	1020	1021
-M42	1100	1101
-M44	1122	1123
-M45	1132	1133
-M46	1204	1205
-M47	1208	1209
-M48	1210	1211
-M49	NT06	NT07
-M50	1300	1301
-M51	1400	1401
-M52	1402	1403
-M53	1404	1405
-M55	1408	1409
-M56	1410	1411
-M57	1412	1413
-M60	1602	1603
-M62	1702	1703
-M64	1706	1707
-M66	1800	1801
-M67	1902	1903
-M68	2000	2001
-M69	2002	2003
-M70	2004	2005
-M72	2300	2301
-M74	2402	2403
-M77	822	823
-M78	2334	2335
-M81	2630	2633
-M81B	2630	2631
-M82	1502	1503
-M84	114a	114b
-M90	21C1	21C2
-M91	22C1	22C2
\ No newline at end of file

Exercises/Project2/Primers.txt

-Name	Sequence
-0022	gcagatgttcgttcaaag
-0023	aggctggattcccaaaac
-0026	gaagctaagaccatacctg
-0027	tggaaacaagagcaatgatc
-0030	atctgtgcaatgttgtgg
-0031	tctgcatgggagagtagg
-00x1	aagttataatgctgatcattggg
-0042	ctcttactacactgctgtc
-0043	gagaccacatagacatgtg
-00x3	ttatctgctaaaatggttgc
-0046	agattagggttctcgggtc
-0047	cgttactataaaaggcgaatac
-00x4	tgcgtaagaactaagagtg
-NT12	AACCCGAGCATTAATTCGTGC
-NT13	CTCTTCCTCAAGTTGTGGCTG
-00x6	ggtgccggtgacgaaaag
-0130	tggacctaaagcatggtac
-0131	gaacacttttgaaagacgag
-01x1	ctacaccggaaaagctagtc00x1
-NT10	CACGTGGCTTGGACTAATTGG
-NT11	CCAACACAGCCTTCACGTAAAG
-02x4	aggattccacattaggactccac
-0206	TTTCTTGTAGCCTCCTCAACC
-0207	TCATTCTCATTTTCCTGAAACG
-02x2	acgtcaagctcgatgcaac
-NT04	TTATCCTATATTTCGAATCCGATTG
-NT05	AACTAAGACTGTCTTTTGGTAAAAT
-03x1	gcagacttctcgcaaacggcagacttctcgcaaacggatcccaactcgggactggaag
-NT22	CGCACCGACAATTCTCTAGCC
-NT23	CTGCTTTTCCCACGTCCTCTC
-03x3	gatcccaactcgggactggaag
-NT26	AAGGGTGTTTGGAGGGAAGTC
-NT27	GTAGCAGCTTTGTAACACCGG
-03x4	gatggatcattttgatggagaaacagg
-NT56	GAGACGCAGGTATTTATAAACTTAT
-NT57	AATCAAACTTGTGAATGAACTAGTA
-03x6	actttggtaaactacgagagc
-0300	AAATCTAATGTTATTGAACAAGTG
-0301	CATCCAACATTACCCCAAACC
-0304	ATACAAGATTCTACCTCGTCG
-0305	ATCCTAAAATCGCAGCTCTTC
-03x7	tctaacgactaaagacattccac
-0424	ctaggcaaaatagccaaac
-0425	tcactagcgaaagctcag
-0426	atggatcgacaacgatgg
-0427	tggtcatcccaattcaac
-0430	ttgtggattctctgttatcc
-0431	cggtaaattaaagcgggac
-NT18	ACACAGAAAACTTCCCCAAGTC
-NT19	TGTTTCTGCTTCGAGACGATC
-NT34	GGATTCAAACATGTCCCGTACC
-NT35	TTGTCTTCCTCACCAAACCCC
-0504	AGTGGTGGAATCTACTTACGG
-0505	GAAAGATTACCTTCAAGGGTG
-05x1	tgatggaccagagttttgg
-0606	GTTTGTATAGTGCCTTAGTGG
-0607	CCACTAATGCTTGATACATCC
-N304	attcactatcgttattacacaagttacctg
-N305	tgtgacgaatgatgcaaaacgag
-0622	tgcttgctacatgacttttg
-0623	ccgaattggtaaaggacc
-0628	aaagatgccacacaaacac
-0629	tgctgacttccccatttac
-06x2	gattcgaatgatagtaaaatgctg
-0704	TGAGTGGGGGTAATTATGTTC
-0705	ATCCGTTTCACATTTTGGTCG
-0708	TGTGCTAGATTACGCTACATC
-0709	CCTTCACCAGAAGATTCTTAC
-0710	CTGAGTCAACCAGATTTGGTC
-0711	CAATGTTTTCAAGCCCGATTC
-0712	AAGTACTGTGCATACGTCATC
-0713	ACATAAGCAGGTCTTAATCCC
-0800	GTGGTGTTTGCCTGTTATGAG
-0801	TTGAGGTGTATTTTGCATGTTC
-08x1	tggacacctacatgtgag
-0820	aggatgaggagtatacagag
-0821	tggtaagtattcccgcttac
-08x2	tcattacccaaacggtgc
-NT16	GCTCATTTGTGTGACCCAAATG
-NT17	ATATTGTTGGAGCGCTTGTGAC
-0900	TAACAATCACTCACAATACATAG
-0901	TCCGATTTTGGTTCAAGATGG
-09x1	agcattacattatgattttaaacg
-1000	TGAACTTGCGTCTTGTTCTTC
-1001	TCATGGTTAAGGGATCTCTGC
-1002	TTTGGTACTAGGCATTCTTGC
-1003	AGATTGATACCATGAGCATGG
-1020	gatgctggtctactccag
-1021	tgaatgtaaacccaagtcg
-10x1	acaggccctaagtatcg
-1100	ACCTCTCGTTTGCTAATCCTG
-1101	TTGCATCATTCTCCTGTGGTG
-11x2	atggaattgcctccaatgc
-1122	taaccattccagcctttc
-1123	cttgttcagagagcaagc
-1132	tgaagcacaaataagtcac
-1133	accaaatattttcaaagttgc
-1204	AGCTACTAAAGACCAATGCTC
-1205	TTCCCCATTACCAATGATTCG
-1208	GTCACTTTCACTCTTTCAGAG
-1209	ACTTAACCGCAGCATCAATAG
-1210	TGAATGTTGAATAGAGGCGAC
-1211	ACTTACCAACCATAGCCATAG
-NT06	TCATATACTCCATAAACTATCTCGT
-NT07	TTGTAAGGGTATGAAAATTCCATTT
-13x1	ccgtgggtacctataatcc
-1300	TTCTCACCAAATAAGAATAGATG
-1301	CGAAATTACCCTCCATGACTC
-1400	TGGTGCAGGTGAGATATATTC
-1401	GATACGAATTTGACCAAATTATG
-14x1	gaacagcccttcacctg
-1402	TCCCTATGTTCATAACTCGAC
-1403	TCGAAGATGGCTTTGACCATC
-1404	ATTAGCCTTCATGTTTCCTCC
-1405	TATCTTCATGGCTTCTCACTC
-1408	GAGATGTTTATGGAAAGCAGG
-1409	CCTAAATAGTTGACTTCAGCC
-1410	GGAATTGTAATCCTTCACCAG
-1411	ACACGTCATGTACTAGTGTCC
-1412	CATTTGCTACGATGGCTAGTC
-1413	GATCAGAAGTCACGATCTTTG
-1602	AACCAAGTAAAACTCAGCCTC
-1603	AAGCTAATCGCTGAGTTATTAC
-1702	TCGACCAGTATACTCGATCAC
-1703	AGATCTCAACAGATCACTCTG
-1706	ACATAATCAACACCGACCTCC
-1707	AGGAAGTTGCTTGGTGATGTG
-1800	TATTGATCAAGTGCAGCCATG
-1801	TCAGATGGATGTACCCATTTG
-1902	TGTTGTGATTTTGGGCCTGAG
-1903	GAAAGGCCAATAGGCTAATGG
-2000	TTTGCTAGATTTGCCTTCTCG
-2001	TAGATATGCATCCAGAACAGG
-2002	TTCGAGTAACCCTGTTACATC
-2003	TCGTTCTTACTCTCAGCAGTG
-2004	ATCGTTTTAACCACCGGTTTC
-2005	ATTCAGACATAACTGGGGCAG
-2300	TTGGTTATCAGTGGAACTGTG
-2301	GCATCCGTTCAAGGAATTAAG
-2402	ACTTCAACAGGGAGATGACAG
-2403	GCACATAACAAGATGTGATCG
-0822	tctgagtgttggggatag
-0823	gaccgtcactaacagtagg
-2334	TTGCACCTTCAAAGGCTG
-2335	TGTGTACATGGCCTGTCG
-2336	CACTCACCTCATCTTGGGAC
-1730	CGGTACTATCTAATGAAGACAAAC
-1731	CGACATCTAACAGAAATCATAAC
-1732	TACTACCTAATTTACGGGAAC
-1733	GACATCTAACAGAAATCATAACG
-2030	CTAACCACTTATGTTCTCTTGC
-2034	GACGAACATCGTCCTCTAG
-2032	CTAACCACTTCTGTTCTCTTAC
-2035	GGACGAACATCATCCTGTAG
-2630	GGTTCTAGTTGTTACTACAAGA
-2631	TCGTTGCATTTTAGTCGG
-2633	TCGTTGCATTTTAGTCCG
-1502	GAGCAGATACCAAAGCATTTG
-1503	TATAAAGGGAGTCTCCACAGG
-114a	TTCACTAAGTATAGCAGCAAGG
-114b	CGAACCTTTTCTCCTAGCCTTC
-114c	GGACAGACACCAAGACAATGC
-21C1	GTCGTAACATTTGGCGACTACG
-21C2	AGACTGCCCGAATCTTTGGAAT
-21N1	GATCAACACATGCTCCCTACCA
-21N2	ATCAGTTACGAAACGACGGACA
-22C1	TCCTCCACCTAAGCCATCACTA
-22C2	AGAAGACGTCGTAGCTAGAGGA
-22N9	TATCGGTGATCATACGGCTTGG
-22N0	TGACAGTGAACTCCTGAATCCG

Exercises/Project2/README.txt

-Project2: in silico- PCR 
-Primer aus einer Datei einlesen und in Referenzseq. suchen, um die PCR-Produktgröße zu bestimmen. Auf Fehlbindungen in anderen Regionen prüfen. Primer formatiert in multiplen FASTA-Dateien ausgeben mit Tm-Wert Berechnungen.

Exercises/Python_course_2021_exercises_B.ipynb

-%% Cell type:markdown id: tags:
-
-# Python course 2021 - Exercises B
-
-
-%% Cell type:markdown id: tags:
-
-## Part1 - control structures
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.1) Write a script for guessing numbers!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.2) Add tips (smaller/larger) during the guessing process!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-## Part2 - loops
-
-%% Cell type:markdown id: tags:
-
-
-
----
-2.1) Write a function counting to 100 and printing all numbers which can be divided by 4 without any residue!
-
-* Info: 10%2    #modulo division in Python
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-2.2) Write a function counting down from 1000 to 0 and printing all numbers!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-2.3) Generate a list of species names! Write a function printing all species names starting with "E"!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-2.4) Expand this function to limit the printing to species names which are additionally shorter than 10 characters!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-2.5) Expand this function to limit the printing to species names which are additionally ending with "a".
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-## Part3 - range & enumerate
-
-%% Cell type:markdown id: tags:
-
-
-
----
-3.1) Write a script to print 50x "here" and the current value of the control variable!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-3.2) Write a script to walk through the species list and to print the character from the species where the index corresponds to the current control variable value!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```

Exercises/Python_course_2021_exercises_C.ipynb

-%% Cell type:markdown id: tags:
-
-# Python course 2021 - Exercises C
-
-%% Cell type:markdown id: tags:
-
-## Part1 - file handling
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.1) Count number of sequences (number of headers) in AtCol0_Exons.fasta!
-
-%% Cell type:code id: tags:
-
-``` 
-from google.colab import drive
-drive.mount('/content/drive')
-```
-
-%% Output
-
-    Drive already mounted at /content/drive; to attempt to forcibly remount, call drive.mount("/content/drive", force_remount=True).
-
-%% Cell type:code id: tags:
-
-``` 
-datei = open("/content/drive/MyDrive/Python_course_2021_data/AtCol0_Exons.fasta", "r")
-lines = datei.readlines()
-datei.close()
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.2) Count number of sequence lines!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.3) Count number of characters in document! (How many per line?)
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.4) How long are all contained sequences combined?
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.5) Calculate the average sequence length in this file!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```

Exercises/Python_course_2021_exercises_D.ipynb

-%% Cell type:markdown id: tags:
-
-# Python course 2021 - Exercises D
-
-%% Cell type:markdown id: tags:
-
-## Part1 - writing files
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.1) Read the file AtCol0_Exons.fasta and write all headers (starting with '>') into a new file!
-
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.2) Read the file AtCol0_Exons.fasta and write the following:
-* Line if it is a header
-* Length of line if it is a sequence line
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.3) Calculate the number of sequences, the cumulative length and the average length in a new file! Are they matching the values of the original file?
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.4) Write sequences into a new file if their length is a multiple of 10!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-## Part2 - characters
-
-%% Cell type:markdown id: tags:
-
-
-
----
-2.1) Read the file AtCol0_Exons.fasta and write the following:
-*   Only Arabidopsis Gene Identifier (e.g. AT1G01010)
-*   Gene Identifier, exon name, exon length (tab-delimited)
-
-
-
-%% Cell type:code id: tags:
-
-``` 
-
-```

Exercises/Python_course_2021_exercises_G.ipynb

-%% Cell type:markdown id: tags:
-
-# Python course 2021 - Exercises G
-
-%% Cell type:markdown id: tags:
-
-## Part1 - easygui
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.1) Write a script to handle input of primer names and sequences! All information should be saved in a multiple FASTA file.
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.2) Write a script to return a matching primer sequence from a FASTA file based on a given primer name.
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-1.3) Write a script to combine both functionalities: return primer sequence, if name is already present OR generate new entry if primer is novel.
-
-%% Cell type:code id: tags:
-
-``` 
-
-```

Exercises/Python_course_2021_exercises_H.ipynb

-%% Cell type:markdown id: tags:
-
-# Python course 2021 - Exercises H
-
-
-%% Cell type:markdown id: tags:
-
-## Operon structure plot
-
-%% Cell type:markdown id: tags:
-
-
-
----
-Construct a figure to illustrate the order and orientation of genes in the gum gene cluster in *Xanthomonas campestris* pv. campestris!
-
-
-
-%% Cell type:code id: tags:
-
-``` 
-
-```

Exercises/Python_course_2021_exercises_I.ipynb

-%% Cell type:markdown id: tags:
-
-# Python course 2021 - Exercises I
-
-%% Cell type:markdown id: tags:
-
-## analyze the unknown data
-
-%% Cell type:markdown id: tags:
-
-
-
----
-Construct a suitable visualization!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-Analyze distribution and trends!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-Apply statistical test to investigate difference!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```

Exercises/Python_course_2021_exercises_J.ipynb

-%% Cell type:markdown id: tags:
-
-# Python course 2021 - Exercises J
-
-%% Cell type:markdown id: tags:
-
-## construct heatmap
-
-%% Cell type:markdown id: tags:
-
-
-
----
-Read data table and construct heatmap for the gene expression!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```
-
-%% Cell type:markdown id: tags:
-
-
-
----
-Display functional gene annotation!
-
-%% Cell type:code id: tags:
-
-``` 
-
-```

Exercises/solutions/Python_course_2022_exercises_REP_1.ipynb

-%% Cell type:markdown id: tags:
-
-# Python course 2022 - Repetition 1
-
-%% Cell type:markdown id: tags:
-
-These exercises are meant for repeating most of what you have learned in the course this far. For most of the tasks, you already have partial solutions from the other exercises. We encourage you to make use of those to review them again and maybe spot room for improvement here and there.
-
-%% Cell type:markdown id: tags:
-
-1.1) Print the current time.
-
-%% Cell type:code id: tags:
-
-``` 
-```
-
-%% Cell type:markdown id: tags:
-
-1.2) Count the number of genes (not exons) in the AtCol0_Exons.fasta file. How many genes are single-exons genes?
-
-%% Cell type:code id: tags:
-
-``` 
-```
-
-%% Cell type:markdown id: tags:
-
-1.3) How many of the genes are located on the forward strand? How many are located on the reverse strand?
-
-%% Cell type:code id: tags:
-
-``` 
-```
-
-%% Cell type:markdown id: tags:
-
-1.4) Count the number of genes per chromosome and plot the results.
-
-%% Cell type:code id: tags:
-
-``` 
-```
-
-%% Cell type:markdown id: tags:
-
-1.5) Count the number of genes located on the chondrom and plastom.
-
-%% Cell type:code id: tags:
-
-``` 
-```
-
-%% Cell type:markdown id: tags:
-
-1.6) Which of the genes may potentially include the amino acid motive "WIP"?
-
-%% Cell type:code id: tags:
-
-``` 
-```