WikiSysop: Created page with "== Answers to "Exercise: Protein databases" == The numbers are found using UniProt on Feb 10, 2017 (release 2017_01). ===Simple text mining=== '''QUESTION 1:''' # How many hits do you find?
3150 # How many of these hits are from Swiss-Prot?
1254 # Can you identify the correct hit (''i.e.'' see which one is actually human insulin and not something else)?
It's P01308 / INS_HUMAN (among the first ten hits). '''QUESTION 2:''' How many hits are now left? How m..."

2024-03-05T11:13:43Z

Created page with "== Answers to "Exercise: Protein databases" == The numbers are found using UniProt on Feb 10, 2017 (release 2017_01). ===Simple text mining=== '''QUESTION 1:''' # How many hits do you find? 3150 # How many of these hits are from Swiss-Prot? 1254 # Can you identify the correct hit (''i.e.'' see which one is actually human insulin and not something else)? It's P01308 / INS_HUMAN (among the first ten hits). '''QUESTION 2:''' How many hits are now left? How m..."

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== Answers to "Exercise: Protein databases" ==

The numbers are found using UniProt on Feb 10, 2017 (release 2017_01).

===Simple text mining===

'''QUESTION 1:'''
# How many hits do you find? 3150
# How many of these hits are from Swiss-Prot? 1254
# Can you identify the correct hit (''i.e.'' see which one is actually human insulin and not something else)? It's P01308 / INS_HUMAN (among the first ten hits).

'''QUESTION 2:''' How many hits are now left? How many of these are from Swiss-Prot? 1298 and 895

'''QUESTION 3:''' How many hits are now left? How many of these are from Swiss-Prot? 195 and 60

'''QUESTION 4:''' How many hits are now left? 100

'''QUESTION 5:'''
# How did you do this? by adding <tt>NOT name:receptor</tt> to the query box.
# How many hits are now left? 48

===The contents of UniProt===

'''QUESTION 6:'''
# How many references are there in the insulin entry? 36
# Why do you think insulin is such a highly investigated protein? Because it is linked to a common and serious disease (diabetes) and used as a drug.

'''QUESTION 7:'''
# Where do you find insulin? It is secreted from the cell (this is written just below the section heading. Under GO - Cellular component you can find additional locations mentioned, such as endoplasmic reticulum lumen, but these are temporary stages on the way to secretion).
# Why do you think is it found there? Because it is a hormone - it has to travel through the bloodstream to influence other cells.

'''QUESTION 8:''' How long is the signal peptide and the propeptide, respectively? 24 and 31 amino acids.

'''QUESTION 9:''' Which positions are in β-sheet conformation in insulin? Positions 26-29, 48-50, 74-76, and 98-101.

===Other databases linked from Swiss-Prot===

''No questions asked here.''

===Advanced search===

'''QUESTION 10:''' How many proteins did you find, and what was the search string (the text in the search field)? 5,186,371 <tt>annotation:(type:signal)</tt>

'''QUESTION 11:''' How many proteins do you find now, and what has the search string changed into? 3486 <tt>annotation:(type:signal evidence:experimental)</tt>

'''QUESTION 12:''' How many proteins do you find now, and what is the search string? 707 <tt>annotation:(type:signal evidence:experimental) AND organism:"Homo sapiens (Human) [9606]"</tt>

'''QUESTION 13 a:''' How many proteins are there in UniProt from ''Neisseria gonorrhoeae'' with the default TaxID [485]? 9203

'''QUESTION 13 b:''' How many proteins are there in UniProt from ''Neisseria gonorrhoeae'' in total (all strains and subspecies)? 18,596 (twice as many)

'''QUESTION 13 c:''' What does the search string look like now? <tt>taxonomy:"Neisseria gonorrhoeae [485]"</tt>.

'''QUESTION 14:''' How many proteins of maximum length 10 do you find? 32,090 <tt>length:[1 TO 10]</tt>

'''QUESTION 15:''' How many proteins are now left? 1280 <tt>length:[1 TO 10] existence:"evidence at protein level"</tt>

'''QUESTION 16:''' How many proteins are now left? 830 <tt>length:[1 TO 10] existence:"evidence at protein level" fragment:no</tt>

'''QUESTION 17:''' How many human non-fragment proteins of maximum length 10 do you find in UniProt? 5 <tt>length:[1 TO 10] existence:"evidence at protein level" fragment:no AND organism:"Human [9606]"</tt>

'''QUESTION 18:''' Here they are in FASTA format:
>sp|P01358|GAJU_HUMAN Gastric juice peptide 1 OS=Homo sapiens PE=1 SV=1
LAAGKVEDSD
>sp|P02728|GLEM_HUMAN Erythrocyte membrane glycopeptide OS=Homo sapiens PE=1 SV=1
CEGHSHDHGA
>sp|P02729|GLUR_HUMAN Urine glycopeptide OS=Homo sapiens PE=1 SV=1
CEHSHDGA
>sp|P22103|PNEU_HUMAN Pneumadin OS=Homo sapiens PE=1 SV=1
AGEPKLDAGV
>sp|P01858|TUFT_HUMAN Phagocytosis-stimulating peptide OS=Homo sapiens PE=1 SV=1
TKPR

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