User: Hamish
Hamish • 3.1k
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I am currently working on a masters in Information and Library Studies. Previously I was a Software engineer for the Web Production team at the European Bioinformatics Institute (EMBL-EBI); a member of the team that supported, developed and maintained SRS at Lion Bioscience Ltd. and worked on genetic and genomic databases for Brassicas at the John Innes Centre.
Posts by Hamish
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... The submitted sequence can be in sense stand or its complement for mRNA sequences. Typically this depends on if the submitter has submitted the raw sequence obtained by sequencing a cDNA library, in which case the submission will be a mixture of sense and complementary strands, or if they have done ...
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... To look-up a protein sequence and find the database identifiers associated with it (i.e. database entries having the same sequence) you can use:
PICR (Protein Identifier Cross-Reference): this service provides options that perform look-up of protein entry identifiers, look-up of protein sequence, ...
written 5.7 years ago by
Hamish • 3.1k
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Comment:
C: Rfam Family Types
... Probably worth contacting the Rfam folks for this, see http://rfam.sanger.ac.uk/help#tabview=tab12
...
written 5.8 years ago by
Hamish • 3.1k
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... PDB ATOM records are not delimited, so the solution suggested by Pappu will not work for all PDB entries. I suggest you see the alternative answer for an option which takes this into account.
...
written 5.8 years ago by
Hamish • 3.1k
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... Assuming that you are just interested in the ATOM records then you will need to take into account the structure of the ATOM records. These are not structured as delimited fields, but are instead position based, thus the identification of the specific chain records must look at a specific position in ...
written 5.8 years ago by
Hamish • 3.1k
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... You can try looking at the EMBL format IMGT/HLA data file which include the exon data (see ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/hla.dat).
For more information about the data provided by IPD (including IMGT/HLA) I suggest you contact the IPD folks via their contact forms:
IMGT/HLA: http: ...
written 5.8 years ago by
Hamish • 3.1k
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... Could just use an EFetch to get the RefSeq entry and extract the sequence type,and description from there using SeqIO. Alternatively you could derive the sequence type from the RefSeq accession (see RefSeq accession numbers and molecule types).
...
written 5.9 years ago by
Hamish • 3.1k
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Comment:
C: Blast2Go Graphs
... For help with Blast2GO from the authors please see:
http://www.blast2go.com/b2gsupport
You can also get help from the community via the Blast2GO Google Group:
https://groups.google.com/forum/#!forum/blast2go
...
written 6.0 years ago by
Hamish • 3.1k
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... From discussions with the EMBOSS developers.
The emboss.open-bio.org site is based on the content written for the EMBOSS books. The aim is to maintain the book content through updates to the emboss.open-bio.org site. While the content generated from the EMBOSS sources has been updated at SourceFor ...
written 6.0 years ago by
Hamish • 3.1k
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... FYI the current EMBOSS documentation and downloads can be found at: http://emboss.open-bio.org/. The old EMBOSS SourceForge site is obsolete.
EMBOSS contains a number of programs related to sequence translation (see B.6.25. Applications in group Nucleic:translation) and gene/ORF finding (see B.6.17 ...
written 6.0 years ago by
Hamish • 3.1k
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4.5 years ago,
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For A: Csharp For Programming In Bioinformatics
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For A: Database Of Host And Pathogen Pairs
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For A: Does Anyone Know How To Cite Ncbi Wwwblast In A Manuscript?
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For A: Speeding Up Psipred (Or Finding A Better Locally-Run Alternative)
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For A: Functional Assessment Of Genes
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5.5 years ago,
created an answer that was upvoted at least 5 times.
For A: Does Anyone Know How To Cite Ncbi Wwwblast In A Manuscript?
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