User: Biojl

gravatar for Biojl
Biojl1.5k
Reputation:
1,530
Status:
Trusted
Location:
Barcelona
Scholar ID:
Google Scholar Page
Last seen:
3 weeks, 4 days ago
Joined:
5 years, 8 months ago
Email:
j********@gmail.com

Biologist

Protein ALignment Optimiser (PALO) is an algorithm for the selection of the best combination of protein isoforms among orthologous genes in the construction of a multiple alignment. You can easily upload your files from ENSEMBL and this tool will tell you which is the most suitable combination for you to align. http://evolutionarygenomics.imim.es/josepl/codeigniter/index.php/pages/view/home http://gbe.oxfordjournals.org/content/5/2/457

Posts by Biojl

<prev • 181 results • page 1 of 19 • next >
1
vote
1
answer
305
views
1
answers
Comment: C: kallisto + sleuth: no results
... Can you paste the full code? ...
written 10 weeks ago by Biojl1.5k
0
votes
1
answer
171
views
1
answer
bulk download in ENCODE
... Hi, I'm trying to download several experiments in bulk from https://www.encodeproject.org/. I use the filters in the experiment matrix and I come up with 97 datasets. I am only interested in bed narrowPeak files (in available data), thus I select only that category. But when I click download I get ...
encode chip-seq download written 3 months ago by Biojl1.5k • updated 3 months ago by tangming20052.2k
1
vote
1
answer
185
views
1
answers
Answer: A: Extract motif ids of all transcription factors in human
... You can programatically access the JASPAR 2016 database using this R package: https://bioconductor.org/packages/release/data/experiment/html/JASPAR2016.html ...
written 4 months ago by Biojl1.5k
3
votes
0
answers
193
views
0
answers
Comment: C: What is the difference between counts and expression level?
... https://www.biostars.org/p/124826/ ...
written 4 months ago by Biojl1.5k
0
votes
1
answer
283
views
1
answers
Answer: A: DESeq2 + de novo assembly
... If you use kallisto you should use Sleuth, which is the DE tool designed for that kind of quantification. Also is easier to use than DESeq2. I would focus on the fraction of transcripts with a blast hit, unless you have very good evidence that there are a number of genes that are not conserved beyo ...
written 4 months ago by Biojl1.5k
4
votes
5
answers
350
views
5
answers
Answer: A: Software for Tree Visualization
... My favourite is [ETE3][1]. You can draw beautiful trees, personalize them to an unprecedented level but most importantly, it allows you to programatically work with trees, asking all sort of questions and even storing information you generate within the trees. A true jewel for researchers working w ...
written 4 months ago by Biojl1.5k
0
votes
0
answers
154
views
0
answers
Mobile elements studied in the 1000 genomes
... Hi, I am trying to download the set of transposable elements for which frequencies were estimated in phase 3. The publication is this one: http://www.nature.com/nature/journal/v526/n7571/full/nature15394.html However, when I download the supplementary material (Table_4_MEIs.xlsx, sheet G) I can s ...
transposable elements 1000 genomes data written 4 months ago by Biojl1.5k
2
votes
1
answer
262
views
1
answers
Answer: A: Long Motif Predicted by MEME SUITE
... What are your input sequences for MEME? ChIP-seq peaks for a particular transcription (which one?) factor perhaps? Which is the species you are working with? Motifs coming from transcription factors are typically 4 to 30 base pairs long, but longer motifs have been described in particular cases. ...
written 5 months ago by Biojl1.5k
0
votes
0
answers
223
views
0
answers
Comment: C: how to get a list of genes affected by a transcription factor?
... Check ENCODE: https://www.encodeproject.org/ ...
written 5 months ago by Biojl1.5k
0
votes
0
answers
223
views
0
answers
Comment: C: how to get a list of genes affected by a transcription factor?
... In which species are your working? ...
written 5 months ago by Biojl1.5k

Latest awards to Biojl

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Where to obtain a gene rpkm matrix for mouse (from mouse encode)
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Obtain conservation (or % ident) in a multiple sequence alignment
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Biostar Ads Are Here! Showcase Your Accomplishments To The World!
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Status Quo: Trinity Vs Oases
Scholar 5 months ago, created an answer that has been accepted. For A: Long Motif Predicted by MEME SUITE
Popular Question 5 months ago, created a question with more than 1,000 views. For Obtain conservation (or % ident) in a multiple sequence alignment
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Status Quo: Trinity Vs Oases
Popular Question 18 months ago, created a question with more than 1,000 views. For Automatic Data Extraction From Timetree
Popular Question 20 months ago, created a question with more than 1,000 views. For Biopython And Codeml Module. Error.
Popular Question 20 months ago, created a question with more than 1,000 views. For How To Parallelize Codeml With Python
Popular Question 20 months ago, created a question with more than 1,000 views. For How To Parallelize Codeml With Python
Popular Question 23 months ago, created a question with more than 1,000 views. For Automatic Data Extraction From Timetree
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Automatic Data Extraction From Timetree
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Where To Get A Mammalian Phylogenetic Tree With Branch Distances.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How To Parallelize Codeml With Python
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Where To Get A Mammalian Phylogenetic Tree With Branch Distances.
Popular Question 3.4 years ago, created a question with more than 1,000 views. For How To Parallelize Codeml With Python
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Status Quo: Trinity Vs Oases
Guru 3.5 years ago, received more than 100 upvotes.
Centurion 3.5 years ago, created 100 posts.
Voter 3.5 years ago, voted more than 100 times.
Supporter 3.5 years ago, voted at least 25 times.
Autobiographer 3.5 years ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1310 users visited in the last hour