User: Mahmut Uludag

gravatar for Mahmut Uludag
Reputation:
10
Status:
New User
Location:
KAUST, Thuwal, Saudi Arabia
Website:
http://www.kaust.edu.sa/
Scholar ID:
Google Scholar Page
Last seen:
7 months ago
Joined:
3 years ago
Email:
m************@kaust.edu.sa

I am interested in improving accessibility and interpretation of research results using open source software technologies such as Solr search platform, Weka Machine Learning library, and R.

I have been working on an open-source project to develop index/query scripts for selected free bioinformatics datasets such as UniProt, HMDB and HGNC. The project has matured to a level that interested researchers can try its development version, installable from Bitbucket and GitHub project pages.

 

Posts by Mahmut Uludag

<prev • 6 results • page 1 of 1 • next >
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Answer: A: Retrieve sequences from uniprot
... Following version of your code returns sequences+isoforms: import requests params = {"query": "P00750", "format": "fasta", "include": "yes"} response = requests.get("http://www.uniprot.org/uniprot/", params=params) print (response.text) ...
written 2.9 years ago by Mahmut Uludag10
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Answer: A: From GI to GO anootations
... - It is likely that some of the entries that has GI numbers are not referenced by any UniProtKB entries, this could be the reason for the 'no results found' messages - As also noted in a recent Biostars post([Question: Cannot download gi list from NCBI protein][1]), NCBI is in the process of [pha ...
written 2.9 years ago by Mahmut Uludag10
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Comment: C: Missing HSPs from Blast xml output
... Probably the error is not because BLAST is looking for the matched sequences in the NCBI database. BLAST is used by many to search local databases, there should not be such bug that breaks the software this way. Sequence with id ... no longer exists error is reported in [showalign.cpp][1] in BLAST ...
written 2.9 years ago by Mahmut Uludag10
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Answer: A: Adding GO:IDs to the BLAST hits
... When I call the mapping step on Blast2Go (v4) I get the following information displayed, under two titles; 'Mapping Configuration'-'Mapping the Blast Hits of each sequence with Gene Ontology Terms'. > Blast2GO performs different mapping steps to link all Blast Hits to the functional information ...
written 2.9 years ago by Mahmut Uludag10
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Answer: A: HOW TO STORE BLAST RESULT INTO DATABASES?
... Once BLAST output is generated in its json output format, it is easy to store these results in MongoDB or Elasticsearch. We have compiled our experience with storing BLAST results in Elasticsearch into an open-source project (https://github.com/uludag/hspsdb-indexer) which has brief documentation. ...
written 3.0 years ago by Mahmut Uludag10
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Answer: A: High Scoring Pairs (HSP) in BLAST output
... Wikipedia BLAST article could be a good read as well; it explains how exact matches are extended to high-scoring segment pairs, how they are evaluated, how alignments are inferred. https://en.wikipedia.org/wiki/BLAST ...
written 3.0 years ago by Mahmut Uludag10

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