User: westin.kosater

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Posts by westin.kosater

<prev • 20 results • page 1 of 2 • next >
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Trying to separate different chains of a PDB file into separate files. Biopython gives an error
... Here is my code parser=PDBParser() io=PDBIO() structure = parser.get_structure('X', '2i0q.pdb') #This will separate each chain into its own PDB file for chain in structure.get_chains(): io.set_structure(chain) io.save(chain.get_id() + ".pdb") Whenever I r ...
python biopython written 8 weeks ago by westin.kosater10
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Python SearchIO: Extracting information from QueryResults?
... I performed a BLAST search of a fasta file with multiple sequences using python. What I want to do now is to extract information and put it in a pandas dataframe. I want the query ID, the hit ID, and the accession number of the hit. Here's what I've done so far: fasta_string = open("list.fasta" ...
python blast xml written 12 weeks ago by westin.kosater10
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Want to loop through list of BLAST objects in python
... I performed a BLAST search with Biopython from a FASTA file with 92 entries (`goat.fasta`) from Bio.Blast import NCBIWWW from Bio.Blast import NCBIXML import pandas as pd fasta_string = open("goat.fasta").read() result_handle = NCBIWWW.qblast("blastx", sequence = fasta ...
python biopython blast written 12 weeks ago by westin.kosater10 • updated 12 weeks ago by finswimmer11k
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Comment: C: CUFFLINKS error: Warning: invalid start coordinate at line:
... Yes, problem is solved ...
written 4 months ago by westin.kosater10
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Answer: C: CUFFLINKS error: Warning: invalid start coordinate at line:
... I discovered my problem. When downloading from the UCSC table browser I did not select GTF file output ...
written 4 months ago by westin.kosater10
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CUFFLINKS error: Warning: invalid start coordinate at line:
... I downloaded a ChIP-seq dataset from ENCODE (ENCFF615OUG.bam) and made an indexed bam file of it (ENCFF615OUG.bai), then extracted the chromosome 22 sequence (chr22.bam) using samtools view samtools view -b ENCFF615OUG.bam chr22 > chr22.bam I need to get FPKM values for genes in chr22, so ...
chip-seq written 4 months ago by westin.kosater10
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Biopython module Bio.PDB.DSSP issue with solvent accessible surface area?
... Hello I am working with PDB files in biopython, and I need a quick way to calculate the relative solvent accessibility (RSA) of each residue in a PDB file. Up until now, I have done it this way from Bio.PDB import * parser = PDBParser() io = PDBIO() structure = parser.get_structure ...
pdb python biopython dssp written 4 months ago by westin.kosater10
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Make a multiple sequence alignment with a HMMER hmmsearch output?
... I have a database of protein sequences and I just did a search (hmmsearch) through the database against my hmmfile using HMMER for all sequence with an E value cutoff. I saved my output from that to a text file, but now I want to do a multiple sequence alignment with the sequences from hmmsearch and ...
hmmer written 5 months ago by westin.kosater10 • updated 5 months ago by h.mon26k
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Trying to interpret the content of a hmm file from HMMER3
... I am working on a homework assignment for a course I am taking. One of the question I am struggling to figure out for myself. What I have done so far is built a HMM model from a sequence with hmmbuild. Here is a short section of that hmmfile as viewed in my text editor HMMER3/f [3.2.1 | June ...
hmmer written 5 months ago by westin.kosater10
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Python: I have a list of probabilities, and I want to use them to generate mutations in a protein sequence
... I have a list of probabilities that I have generated. Here is a short snippet of what this variable looks like [0.62, 0.20. 0.0, 0.69, 0.24, 0.50, ...] These are probabilities that an amino acid substitution will happen in a protein sequence. What I want to do is to take this list of probabili ...
pdb python dssp written 5 months ago by westin.kosater10 • updated 5 months ago by e.benn110

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Scholar 4 months ago, created an answer that has been accepted. For C: CUFFLINKS error: Warning: invalid start coordinate at line:

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