Difference between revisions of "Biopython/C2/Parsing-Data/English-timed"

| In this tutorial, we will learn to, Download '''FASTA''' and '''GenBank''' files from '''NCBI''' database website.

| And '''Parse''' data files using functions in '''Sequence Input/Output''' module.

| To follow this tutorial you should be familiar with, Undergraduate Biochemistry or Bioinformatics

| And basic '''Python''' programming  

| To record this tutorial I am using '''Ubuntu''' OS version. 14.10

| '''Python''' version 2.7.8

| '''Ipython interpretor''' version 2.3.0  

| '''Biopython''' 1.64 and '''Mozilla Firefox '''browser 35.0

| Scientific data in biology is generally stored in text files such as '''FASTA''', '''GenBank''', '''EMBL''', '''Swiss-Prot''' etc

|In the search box type, '''human insulin''' click on search button.

| The web-page shows many files for human insulin gene.

|For demonstration, I will select 4 files with the name “'''Homo sapiens Insulin mRNA”. '''

|I will choose files that have less than 500 base pairs.

|Click on the check box to select the file to download.

|Click on the small selection button with a down arrow present next to the “'''Send to'''” button.

| Under the heading “'''Choose destination'''” Click on “'''File'''” option.

|You can save this file in any file format listed under “'''format'''” drop down list box.

|Choose “'''FASTA'''” from the given options.

|Then click on “'''Create file'''” option.  

| A dialog box appears on the screen.  

|Select “'''Open with'''” click on '''OK .'''

| A file opens in a text editor.

|The first line in each record is an '''identifier''' line,

|It starts with a “greater than (>) symbol”.

|Save the file in your home folder as “'''sequence.fasta'''”.

| Follow the same steps as above to download the files in '''GenBank''' format

|For the same files selected earlier.

|Select the file format as '''GenBank.'''

|Save the file as '''sequence.gb '''in your home folder'''.'''Close the text editor'''.'''

|Now select the file “'''Human insulin gene complete cds'''”.

| And Follow the same steps shown earlier to save the file in the home folder.

|Most file formats can be parsed using functions available in '''SeqIO''' module.

|Most commonly used functions of '''SeqIO''' module are, '''parse''', '''read''', '''write''', and '''convert'''.

| Open the terminal by pressing '''ctrl''', '''alt''' and '''t''' keys simultaneously.

| Start '''Ipython''' by typing '''ipython''' at the prompt. Press enter.

| Next import '''SeqIO''' module from '''Bio''' package.

| At the prompt type,'''from Bio import SeqIO'''. Press enter

|Notice that we have used '''read''' function instead of parse function. Press Enter

|At the prompt type, '''record dot seq '''. Press enter

| To view the identifiers for this record, type, '''record dot id.''' Press enter

|You can use the function described above to parse the data files of your choice.

| Now Let's summarize,

|In this tutorial we have learnt, to Download '''FASTA''' and '''GenBank''' files from '''NCBI''' database website, and use '''parse''' and '''read''' functions from the '''SeqIO''' module:

|To extract data such as record ids, description and sequences, from '''FASTA''' and '''GenBank''' files.

| Now for the assignment,

|Use '''parse''' function to load nucleotide sequences from the '''FASTA''' file.

|Next print reverse complements using the Sequence object’s built in reverse complement method.

| Video at the following link, summarizes the spoken-tutorial project.

| The Spoken Tutorial Project Team Conducts workshops and gives certificates to those who pass an on-line test.  

|More information on this Mission is available at the link shown.  

|This is Snehalatha from IIT Bombay signing off. Thank you for joining.