User: marghe08

gravatar for marghe08
marghe0810
Reputation:
10
Status:
New User
Location:
Last seen:
1 year, 11 months ago
Joined:
2 years, 9 months ago
Email:
m***********@alice.it

Posts by marghe08

<prev • 11 results • page 1 of 2 • next >
2
votes
1
answer
586
views
1
answer
convert bash code to python
... From terminal I launch this command to test the specificity of a pair of primers. MFEprimer.py -i <(echo -e ">pf\nAGTTTTTGCATTCTAGTG\n>pr\nTGTTAGCAATTTCAACAG") -d human.dna --tab How do I translate this command into python code? Thank you in advance. ...
python specificity primer written 23 months ago by marghe0810
1
vote
1
answer
922
views
1
answer
Obtaining .bed list of exons of chr17
... I would like to download/build a simple .bed file with all the exon regions oh chr17. Can anyone help me with that? Thank you in advance. ...
bed exon written 2.3 years ago by marghe0810 • updated 2.1 years ago by Alex Reynolds28k
0
votes
0
answers
921
views
0
answers
primer3: calcHeterodimer between two primers
... For the thermodynamic characterization of the primers I'm using: https://pypi.python.org/pypi/primer3-py/0.3.0 I'm considering the problem of dimerization between the primer, using the calcHeterodimer function. This is an example: >>> res = calcHeterodimer('CCGACCCTATGGGACC', 'TTGGTCCCATA ...
python primer3 written 2.6 years ago by marghe0810
0
votes
0
answers
969
views
0
answers
primer3-py Gibbs free energy
... I'm using primer3-py0.3.0, the Python bindings for Primer3. I have a sequence "S" that is my candidate primer: I want to see if Gibbs free energy of the last five bases of the primer at the 3' is greater than -9kcal/mol. There is a function "calcEndStability" that "Calculate the 3’ end stability of ...
gibbs python primer3 written 2.6 years ago by marghe0810
0
votes
0
answers
570
views
0
answers
read "exon_id" file genbank
... I have a file genbank. I have the following problem: exon complement(80983..81065) /note="exon_id=ENSE00001896310.1" in python, I want to extract the value of the "exon_id " (the value, in the example above, is "ENSE00001896310.1") ...
python genbak written 2.6 years ago by marghe0810
0
votes
0
answers
863
views
0
answers
Comment: C: filter repeated region
... I'm using locally the human genomic database. I would like to have only the human genomic contig sequences with NT _ #### Accessions or CM_##### ...
written 2.7 years ago by marghe0810
1
vote
0
answers
863
views
0
answers
filter repeated region
... I'm using blastn locally. The database that I use is "human_genomic". How can I filter the repeated region of the genome? ...
blast blastn written 2.7 years ago by marghe0810 • updated 2.7 years ago by Biostar ♦♦ 20
0
votes
1
answer
850
views
1
answers
Comment: C: query in human_genomic database
... The version is BLASTN 2.2.31+ I don't get any error message, the only message I get is "Killed". The human_genomic database is 11Gb. Do I require any particular RAM requirements? Do I require at least 11 GB of free RAM? ...
written 2.7 years ago by marghe0810
1
vote
1
answer
850
views
1
answer
query in human_genomic database
... Hello to all. I present my problem. In my computer I have downloaded the "human_genomic database" from the ncbi site and then unzipped the various files. I have a fasta file "BRCA1.fa" that contains a nucleotide sequence. The command that I launched in unix terminal is: blastn -query = BRCA1.fa ...
blast blastn written 2.7 years ago by marghe0810 • updated 2.7 years ago by mastal5112.0k
0
votes
1
answer
620
views
1
answer
querying a database with a substring contained in a file fasta
... Hello! I present my problem. I created with the command "makeblastdb" a database that contains my sequences of interest. Now I want to make a query: the file on which do the query (assume it's called NG_006672.fasta) contains a single sequence; I want to make a query on a substring of the sequence ...
blastdb blast query written 2.8 years ago by marghe0810 • updated 2.8 years ago by shenwei3564.8k

Latest awards to marghe08

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1640 users visited in the last hour