User: Lalla

gravatar for Lalla
Lalla40
Reputation:
40
Status:
New User
Location:
Germany
Last seen:
10 months, 2 weeks ago
Joined:
5 years, 2 months ago
Email:
a**********@gmail.com

Posts by Lalla

<prev • 23 results • page 2 of 3 • next >
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Answer: A: Protein ID and Protein domain ID description
... Thanks, but I have to do the opposite, I have a list of different domain Ids from different databases and I would like to find their description without enter each single ID (or group of IDs of a same type) into the respective database. Those IDs are a results of a Perl Ensembl API query, maybe the ...
written 5.1 years ago by Lalla40
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Answer: A: Protein ID and Protein domain ID description
... Thanks a lot! ...
written 5.1 years ago by Lalla40
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Protein ID and Protein domain ID description
... Hi! Given a list of protein IDs how can I retrieve the description and information (for example protein domains) related to them in a systematic way? Specifically I'd like to know how 2 different proteins from a same gene differ in their domains, structure and function. Is there a database I can ...
protein domain protein written 5.1 years ago by Lalla40
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Answer: A: exon pfam domain overlap
... Hi! I am doing exactly the same thing, I tried different approaches but the easiest and most effective, in my opinion, is the query with API ensembl. If you didn't do it yet, try to have a look at it (http://www.ensembl.org/info/docs/index.html) and related tutorials (http://www.ebi.ac.uk/training/ ...
written 5.1 years ago by Lalla40
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Retrieve protein domain coordinates given a protein/transcript ID
... Hi! I have a list of ensembl transcript and proten IDs and I want to find the coordinates of the protein domains of these proteins. Is there a tool which allows me to find this information given the protein or transcript IDs as an input? My ultimate goal is to find if the exons that I am studying a ...
protein domains coordinates written 5.2 years ago by Lalla40 • updated 2.5 years ago by Jean-Karim Heriche22k
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Comment: C: Hg19 Coordinate To Cds Position
... Hi! I'm dealing with the same issue, could you please write how you adapted the code of mapToTranscript to get the PROTEINLOC? and how can I refer the code to my own dataset (I have hundreds of differentially expressed exons with their genomic coordinates in a csv file)? Thanks!   ...
written 5.2 years ago by Lalla40
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Answer: A: Problem with different release of Ensembl
... Thanks. It juste seemed too odd that all the regions that I looked at were disordered, but that might be the case. Thanks for all the help!   ...
written 5.2 years ago by Lalla40
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Comment: C: Problem with different release of Ensembl
... This is the output with Emboss 6-pack >EMBOSS_001_1_ORF1 Translation of EMBOSS_001 in frame 1, ORF 1, threshold 1, 485aa MSLPEKQPAALTAALAAEDEQLSKGNPPECGMDSRKEIGQDGFEWQRTEGKLNEIGLNVS MDGQLKDRLVKNSSFLEQNKLGFFEGKLDKELSIEKPNKAYQETSGHLESGYVISGTCQP SEGNLVHQKAAEFHPGLTEGKDKAATVQGKVAGKSGLEIKSQPDLNFPGAA ...
written 5.2 years ago by Lalla40
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Comment: A: Problem with different release of Ensembl
... Hi! Thank you very much for your reply and for have posted the release 61. I have to apologize, I was using Biomart with my regions of interest and I didn't realize that when I select exons sequences it gives the sequences of all the exons of the genes which contain these regions and not only the s ...
written 5.2 years ago by Lalla40
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Comment: C: Problem with different release of Ensembl
... Thanks! and sorry for the mistake :)   ...
written 5.2 years ago by Lalla40

Latest awards to Lalla

Popular Question 11 months ago, created a question with more than 1,000 views. For Ensembl retired transcript IDs
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Ensembl retired transcript IDs
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Isoform switch, definition and selection of candidates
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Protein ID and Protein domain ID description
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Protein ID and Protein domain ID description
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Isoform switch, definition and selection of candidates
Student 5.0 years ago, asked a question with at least 3 up-votes. For Retrieve protein domain coordinates given a protein/transcript ID

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