Lecture 1
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Questions and Answers

Which of the following is required to run a Python program?

  • A web browser
  • A Python interpreter (correct)
  • A Java compiler
  • An HTML file

    • Python programs can only use English language keywords.

    True

    What command is used to output 'Hello world!' in a Python program?

    print('Hello world!')

    In Python, a _____ is used to represent a collection of key-value pairs.

    <p>dictionary</p> Signup and view all the answers

    Match the following Python built-in types with their examples:

    <p>Integer = myNumber=1 Float = myFloat=2.1 List = myList=[1,2,3,'four'] String = myString='biotech'</p> Signup and view all the answers

    Which operator is used in Python to calculate the modulus?

    <p>%</p> Signup and view all the answers

    The flow control structure in Python includes if/elif/else statements.

    <p>True</p> Signup and view all the answers

    What is the purpose of the break statement in Python?

    <p>To exit a loop prematurely.</p> Signup and view all the answers

    What is the primary organism referenced in the sequence?

    <p>Drosophila melanogaster</p> Signup and view all the answers

    The Bio.SeqIO module is designed for input and output of various sequence file formats.

    <p>True</p> Signup and view all the answers

    What is the goal of using the Basic Local Alignment Search Tool (BLAST)?

    <p>To find similarities between known sequences and unknown sequences.</p> Signup and view all the answers

    BioPython allows users to convert DNA sequences among different __________.

    <p>formats</p> Signup and view all the answers

    Match the following BioPython modules to their main function:

    <p>Bio.SeqIO = Input and output of sequence file formats Bio.SearchIO = Searching sequences against databases Bio.Align = Sequence alignment Bio.Blast = Performing BLAST searches</p> Signup and view all the answers

    What does the FASTQ format primarily include along with DNA base calls?

    <p>Quality scores or Phred scores</p> Signup and view all the answers

    Multiple FASTA records can be combined in a single file.

    <p>True</p> Signup and view all the answers

    What is the first line of a FASTQ entry always start with?

    <p>@</p> Signup and view all the answers

    A FASTA record should not mix _____ and _____ records in the same file.

    <p>DNA, protein</p> Signup and view all the answers

    Match the following sequence formats with their characteristics:

    <p>FASTA = Includes only nucleotide or protein sequences FASTQ = Includes quality scores for sequencing accuracy Genbank = Provides detailed metadata along with sequence information CSV = Commas separate values without specific standards</p> Signup and view all the answers

    Which of the following is NOT a component of a FASTQ entry?

    <p>Protein structure data</p> Signup and view all the answers

    The third line of a FASTQ entry is represented by a plus symbol (‘+’).

    <p>True</p> Signup and view all the answers

    What type of information does the Phred score represent?

    <p>Quality of base calls</p> Signup and view all the answers

    In Genbank format, the LOCUS line provides information about the sequence's _____ and _____ type.

    <p>length, molecular</p> Signup and view all the answers

    Which line of a FASTQ entry contains the actual DNA base calls?

    <p>Line 2</p> Signup and view all the answers

    What is the source organism of the accession AY069118?

    <p>Drosophila melanogaster</p> Signup and view all the answers

    Internal priming is a known artifact associated with cDNA clone generation.

    <p>True</p> Signup and view all the answers

    What may contaminants during cDNA generation lead to?

    <p>priming from contaminating genomic DNA</p> Signup and view all the answers

    The accession number of this cDNA clone is ______.

    <p>AY069118</p> Signup and view all the answers

    Match the following attributes related to cDNA generation with their corresponding descriptions:

    <p>Internal priming = May interfere with accurate cDNA synthesis Reverse transcriptase errors = Can cause single base changes in cDNA Retained introns = Result from transcription of unspliced precursors Contaminating genomic DNA = Can lead to incorrect priming</p> Signup and view all the answers

    Which of the following is a potential artifact from reverse transcription of precursor RNAs?

    <p>Single base changes</p> Signup and view all the answers

    The information about the sequence can be found on a web page or via email.

    <p>True</p> Signup and view all the answers

    What does cDNA stand for?

    <p>complementary DNA</p> Signup and view all the answers

    The genetic material of fruit flies belongs to the kingdom ______.

    <p>Eukaryota</p> Signup and view all the answers

    Which domain of life does Drosophila melanogaster belong to?

    <p>Eukarya</p> Signup and view all the answers

    Study Notes

    Course Details

    • Course Title: BIOTECH4BI3 - BIOINFORMATICS
    • Lecture 1: Python review and introduction to BioPython

    Python Installation

    • Use Anaconda: www.anaconda.com/products/individual
    • Download Python 3.12 version suitable for your platform (Windows, Mac, Linux)
    • Install the appropriate installer (different versions for Windows, Mac, and Linux). Windows has a 64-bit Graphical Installer (912.3M), Mac has a 64-bit (Apple silicon) Graphical Installer (704.7M), and Linux has a 64-bit (x86) Installer (1007.9M).

    Python Fundamentals

    • Extensive standard library
    • Promotes easy addition of new functionality
    • Code structure is crucial
    • Proper use of English language keywords is essential (e.g., capitalization matters)
    • "Clever" coding is not considered a positive attribute

    Hello World! Example

    • Each Python program typically starts with a declaration specifying the Python interpreter's location (often omitted on Windows)
    • Use \n for newline characters
    • Strings for text need quotation marks
    • Save the program with a .py extension
    • Execute the program using the python command

    Data Types

    • Python has built-in data types, including numbers (integers and floats) and strings
    • Variables store data (e.g., myNumber = 1, mySentence = "You will love my class")
    • Operators for data manipulation (e.g., +, -, *, /, %, **, <=, >=, !=, <, >).

    Built-in Python Types

    • Integers (int(x))
    • Floats (float(x))
    • Lists (e.g., myList=[1,2,3,'four'])
    • Ranges (e.g., myRange=range(0,10,2))
    • Strings (e.g., myString="biotech")
    • Dictionaries (e.g., myHash={'Joe':123,'John':456})

    Flow Control

    • Python uses familiar constructs (e.g., if/elif/else, for statements, while statements, break, continue) for program flow control.

    If/elif/else

    • Conditional statements provide choices to actions
    • If condition is true, execute operation 1
    • If condition is false but elif condition is true , execute operation 2
    • If neither condition is true, execute operation 3

    For Loop Examples

    • Used for looping through a defined or specified range
    • Avoid infinite loops (ensure your loop counter changes value).
    • Use indentation to structure your code within the loop

    While Loop Examples

    • Used for looping an indeterminate number of times
    • The while loop continues executing as long as the logical value is True. Make a condition that changes from True to False to end the loop.

    Lists

    • List is a data structure for storing objects sequentially
    • Create a list (e.g., myList = [])
    • Add elements (myList.append(element))
    • Add lists to lists (myList.extend(listToAppend))
    • Insert elements (myList.insert(index, element))
    • Delete elements (del myList[index], myList.pop(index))

    Dictionaries

    • A data structure for key-value pairs
    • Create an empty dictionary (myBook = {})
    • Add key-value pairs (myBook["one"] = 1)
    • Delete key-value pairs (del myBook["one"], myBook.pop("one"))
    • Accessing keys, values, and key-value pairs (myKeys=myBook.keys(), myValues=myBook.values(), for key, value in myBook.items())

    Files

    • Python has an easy way to access text files
    • Use FILEHANDLE = open(FILE, mode='r') to open the file for reading
    • FILEHANDLE = open(FILE, mode='w') to open to write, and FILEHANDLE = open(FILE, mode='a') for appending
    • Reading a line from the file (myLine = myFile.readline())
    • Writing to a file (myFile.write(“This is a text”))
    • Closing the file (myFile.close())

    Miscellaneous Commands

    • str.rstrip() : Removes whitespace from the end of a string (by default). Can also remove newlines (\n) using str.rstrip('\n')
    • ''.join(list): Joins the strings in a list into a single string.
    • str.split() : Splits a string into a list of strings.
    • str.find(): Finds the position of a substring within a string.
    • str.replace(old,new) : Replaces occurrences of 'old' with 'new' in a string
    • Replacing characters at specified positions (stringList[index]=newCharacter)

    Error Handling

    • A try...except block handles potential errors gracefully
    • try block: Code that might raise an error.
    • The except block: Handles the specific error type.
    • finally block: Always executes regardless of errors, often for cleanup operations.

    Command-line Arguments

    • Pass information to a Python program at execution
    • sys.argv stores the arguments
    • programName = sys.argv[0] access file name
    • arg1=sys.argv[1] access the first external argument input

    Python Functions

    • Reusable code blocks
    • def FUNCTION_NAME(PARAMETERS): to define a function
    • RETURN_VALUE to return data or execute an action

    BioPython

    • A collection of Python classes designed to handle bioinformatics tasks
    • Facilitates processing BLAST reports and other bioinformatics data
    • Useful for working with DNA sequences and converting between different formats (e.g., Genbank, FASTA, FASTQ

    FASTA Format

    • Standard format for DNA data exchange in bioinformatics.
    • Each record starts with a ">" followed by a descriptive title.
    • DNA data starts on the next line.

    FASTQ Format

    • Used for high-throughput DNA sequencing data.
    • Contains base calls and quality scores.
    • Each record has four lines:
      • The first line begins with an "@" symbol; provides identifying information.
      • The second line contains the DNA base sequence.
      • The third line begins with a "+" character.
      • The fourth line shows quality scores for corresponding bases.

    Genbank Format

    • Widely used format for nucleotide data in bioinformatics.
    • Contains various metadata about the sequence including location, accession numbers, and references.

    Bio.SeqIO

    • A module in BioPython for parsing and writing sequence files in different formats.
    • Often used for processing FASTA, GenBank, and other formats.

    Bio.SearchIO

    • Used to search a sequence against a database of sequences, specifically through programs like BLAST.
    • Converts and processes results from BLAST reports.

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    Bioinformatics Lecture 1 on Python PDF

    Description

    Test your knowledge of Python programming and its applications in bioinformatics. This quiz covers essential Python concepts along with specific BioPython modules and file formats used in biological data analysis. Perfect for learners who want to assess their understanding of these two critical areas.

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