User: Hmm

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Hmm490
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490
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4 years, 7 months ago
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Posts by Hmm

<prev • 40 results • page 1 of 4 • next >
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How To Map Ucsc Ids To Uniprot?
... I have a list of ucsc ids such as: uc003tlo.1 uc010fmh.2 uc010fmh.2 uc010fmh.2 uc010fmh.2 uc010fmh.2 uc010srq.1 uc010srq.1 uc010snr.1 uc002cpk.1 uc001vwc.3 uc001vwc.3 uc001vwc.3 uc009vwl.2 ... ...... ......... How can i map them to uniprot ids. One way i thought was possible was to download the u ...
ucsc mapping uniprot written 4.6 years ago by Hmm490 • updated 4.6 years ago by Pierre Lindenbaum106k
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How To Map Peptides To Genomic Locations (Hg19)
... Is there a reliable tool to map the following sample peptides to genomic locations: NMGGPYGGGNYGPGGSGGSGGYGGR SQSSGSSATHPISVPGAR HTGPNSPDTANDGFVR NMGGPYGGGNYGPGGSGGSGGYGGR SKSQSSGSSATHPISVPGAR SHHAPMSPGSSGGGGQPLAR GSGTASDDEFENLR ..... .............(many other peptides) I am interested in the gen ...
coordinates genomic map written 4.7 years ago by Hmm490 • updated 4.7 years ago by SRKR160
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Answer: A: Download Older Versions Of Refseq?
... Actually the easiest way is through commandline: This Works. curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NM_001101.2,NM_001568.1,NM_001904,NM_001973.2,NM_001986.1,NM_001987.3,NM_002015.2,NM_002017.2,NM_002520.4,NM_002584.1,NM_002608.1,NM_002701.3,NM_002844 ...
written 4.7 years ago by Hmm490
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Comment: C: Download Older Versions Of Refseq?
... @Hamish: Thanks. Although it is in the current version but when i access an id such as NM_005656.1 it displays a message: "This sequence has been updated. See current version." The issue is i downloaded the whole mrna_refseq latest version and could not locate the id NM_005656.1 in it. ...
written 4.7 years ago by Hmm490
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Download Older Versions Of Refseq?
... I am trying to bulk download or programmatically access the FASTA file for the following refseq IDs (which are from the older Refseq version): NM_005656.1 NM_016211 NM_015668.3 NM_014584.1 NM_001134673.3 NM_001040454 NM_138799.2 NM_002880.3 NM_001098811.1 NM_014447.2 NM_033547.3 NM_032360.3 NM_0151 ...
fasta refseq written 4.7 years ago by Hmm490
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Can We Use Rnaseq Fpkm Values Derived From 18 Cellines And Run Gsea Analysis On It?
... I have 2 questions: 1) I have FPKM values for each cell line. How do i further normalize the results so that i can compare across cell lines. Do i do a zscore/robust zscore for each celline? 2) Has anyone ran GSEA software from the broad institute n RNAseq data and if yes, then is the input to GSEA ...
rnaseq fpkm written 4.8 years ago by Hmm490 • updated 4.8 years ago by Damian Kao14k
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How To Reduce The Number Of Genes For A Microrray Experiment Done On Cell Lines (Dimensionality Reduction)?
... I have a dataset with 18 cell lines (HG_U133_plus2) normalized using GCRMA. I have collapsed the dataset to genes using the median of the probes. Before proceeding further with any kind of differential expression, how do you guys deal with more than 20 thousand genes. Do you remove genes that hav ...
microarray written 4.8 years ago by Hmm490 • updated 4.8 years ago by hanguangchun120
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Running Blastp From Biopython And Only Looking For Exact Matches
... I have protein sequences that i split at every 'R' and convert them to peptides. Currently it searches for perfect and non perfect alignments. What i wanted to accomplish is: 1) Rather than searching one by one, is there a way to batch all these peptides and send them? 2) Find perfect match only ...
fasta biopython written 4.9 years ago by Hmm490 • updated 4.9 years ago by Biojl1.6k
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Answer: A: Suggesting The Removal Of Post Closing
... a couple of years ago when i joined biostars, the community was friendly and most questions were answered by intelligent people. No matter what kind of question! But now there are moderators that pounce on you make you feel like dumb bioinformatician asking a stupid question .I think the whole idea ...
written 4.9 years ago by Hmm490
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How To Interpret Fusion Genes In Hgvs Format From Cosmic Database?
... For example what does this mean exactly: SRGAP3{NM_014850.1}:r.1_1538_SRGAP3{NM_014850.1}:r.1511_1538_RAF1{NM_002880}:r.964_2977 or EML4{ENST00000318522}:r.1_1943_ALK{NM_004304}:r.4151_6222 There is some documentation @ the following website but still i donot get what the fusion genes exactly ...
fusion genes written 4.9 years ago by Hmm490 • updated 2.1 years ago by Jessica L0

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