Open google homepage, search VecScreen, enter VecScreen homepage, copy sequence, run and view report.
Second, the results:
The output sequence length is 9 18bp,
The region of the vector sequence is 456 BP-854 BP.
Cloning vectors: M 13mp 18 phage, pGEM- 13Zf(+), pBR322, pRKW2.
2. Use the corresponding tools to analyze the repeated sequences of the subsequent unknown sequences, and output the area of the repeated sequences, the types of all repeated sequences, the total length of the repeated sequences and the mask sequences.
First, the steps are:
Go to Google home page, go to ICBI home page, burst sequence. The sequence is human.
Go to google homepage, search RepeatMasker, go to RepeatMasker homepage, go to RepeatMasking, copy sequence, select human from DNA source, and run! Click the hyperlink and select from the results.
Annotation file: rm2sequepload _1287631711.out.html.
3. Using CpGPlot/CpGReport/Isochore tool, analyze the following unknown sequence, and output the length, area, GC number, percentage and Obs/Exp value of CpG island. First, the steps are:
Go to google homepage, search CpGPlot, go to CpGPlot homepage, select cpgreport replication sequence in the program, and run!
Second, the results:
CpG island length: 385bp.
Area: 48-432;
GC quantity: total C+G=297, percentage =77. 14.
Obs/Exp: 1.0 1
4. Predict the promoter of the following sequence, and output the possible promoter sequences and corresponding positions. First, the steps are:
Go to Google home page, go to ICBI home page, burst sequence. The sequence is human.
Go to google homepage, search neural network promoter prediction, go to homepage, copy sequence, select eukaryote, and run!
Second, the results:
Location: 711-761,1388-1438,1755-1805;
5. Analyze the following sequences by using the splicing site prediction tool, and output the donor and acceptor regions of intron-exon splicing site and the bases of splicing site respectively. First, the steps are:
Go to Google home page, go to ICBI home page, burst sequence. The sequence is human.
Go to Google homepage, search for splice site prediction, go to homepage, copy sequence. Organizations choose humans or others. Other defaults, run!
Second, the results:
Donor:
Receptor:
6. Carry out six-frame translation of the following sequence, comprehensively analyze which ORF is correct by GENESCAN (first determine the species source of the given sequence), and output six-frame translation (screenshot) and GENESCAN results (including predicted gene/exon and predicted peptide sequence). First, the steps are:
Go to Google home page, go to ICBI home page, burst sequence. The sequence belongs to Zea.
Enter the Google home page; Search NCBI, enter the home page, select all resources (A~Z), select O, and select Orfpinder. Copy sequence, default, run!
Results: ORF diagram
Third, steps: enter the google home page, search for GENESCAN, enter the home page, organize: size and other defaults, run!
Fourth, the result:
G7。 Enter the database of REBASE restriction endonucleases, and output the identification sequences and types of three endonucleases: AluI, MboI and EcoI.
1. step: enter google homepage, google in English, search REBASE, enter the homepage, enter AluI, MboI and EcoI respectively, and run!
Select the first one in MboI and the second one in EcoI.
Second, the results:
Enskantu
8. Using the primer design tool, design a pair of primers for the following unknown sequences. The required primer length is 20-25bp, the amplified product length is 300-500bp, and the annealing temperature is 50-60℃. Please write down the selected primer pair (forward primer and reverse primer), and the corresponding GC content, primer site, Tm value and product length. 1. step: go to google homepage, search for genefisher, go to homepage, copy fasta format, chechk input, sunmit,; ; Set that length of the primer to be 20-25bp, the length of the amplify product to be 300-500bp, and the annealing temperature to be 50-60 DEG C; .
Second, the results:
GC content:
Primer position:
Tm value:
Product length:.
9. Analyze the following sequence with NEBcutter 2.0 tool, cut it with blunt-ended and four-cleavage-site enzymes, and submit it to view gel with snapshot. Require 1.4% agarose and DNA ladder labeled100bp.
First, the steps are:
Go to the Google homepage, go to the ICBI homepage, and explode the sequence, knowing that it is linear.
Go to Google homepage, search NEBcutter 2.0, go to homepage, select Linear, and run! Select custom summary, change "1" to "4", select flat end, and then select summary. Check the gel. Select 1.4% agarose and mark it as 100bp.
Second, the results:
Then protein's. In general, swiss-prot is suitable for searching and calculating pi/mw to find theoretical molecular weight. Physical and chemical properties of protparam. Quality analysis of hydrophilic and hydrophobic peptides of endoprotease treated with protease and chemical reagents.
NCBI-GenBank database
Database Similarity Search —— Comparison between Nucleic Acid Sequences and Nucleic Acid Database (BLASTN)
Comparison between protein sequence and protein sequence in database (BLASTP)
Align two sequences.
DNA sequence analysis-Offende (www.ncbi.nlm.nih.gov/gorf/gorf.html)
The exon -genscan (/nebcuter2/index.php) of the experimental sequence was analyzed.
Note: Customize Summary-View Gel
Restriction endonuclease database -rebase (/rebase/rebase.html)
Design the experimental sequence of primer amplification-gene Fisher
Primer 3
Protein sequence analysis and structure prediction;
1. Predict the molecular weight and isoelectric point of protein: ExPASy (calculate pI/Mw).
2. Analyze the basic physical and chemical properties of protein: ExPASy(ProtParam).
3. Analyze the hydrophilicity and hydrophobicity of protein: ExPASy(ProtScale).
4. Analyze protein's endonuclease product: EXPASY (peptide mass) [*: kinase K] after being treated by various proteases and chemical reagents.
5. Analyze protein's signal peptide: ExPASy(SignalP).
6. Predicting the secondary structure of protein: ExPASy(Jpred 3)
Phylogenetic analysis of multi-species molecular systems: EMBL(www. ebi. AC. uk/EMBL/)- Toolbox -Clustal2w
Protein sequence of human adiponectin: NP_004788.
Precursor of human insulin growth factor IB: P050 19