User: arunprasanna83

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Posts by arunprasanna83

<prev • 23 results • page 1 of 3 • next >
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Data requirement for gene regulatory network
... Hello, I have only RNASeq data for two conditions control and test (not a time series). Is it possible to identify gene regulatory networks ? If not, what are the minimum required datasets needed to construct one ? Kindly help me the way forward. Thanks, AP ...
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Annotation of taxonomy information in phylogeny tree
... Hello, I have a phylogenetic tree with 85 species. I wish to annotate them with 'Class or phylum' information as branch label. Can anyone suggest a tool available ? ofcourse not with paint ! Is it possible in ETE toolkit ? Thanks, AP ...
phylogeny annotation tree ete written 5 months ago by arunprasanna8320 • updated 5 months ago by jhc2.7k
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Protein blastp .pin file warning
... Hello, I have recently run a blastp. My database size was 1.6 GB. I ran my query and got the output (~300MB). However, I noticed that, the log file had warning lines ..Unable to open *.pin file. My concern is that, is this a serious case? i.e would it have affected BLAST results ? Thanks in Adva ...
protein blast written 11 months ago by arunprasanna8320 • updated 11 months ago by Biostar ♦♦ 20
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Locate for pattern in protein sequence with Biopython
... Hello, I am trying to find sequences that has a tripeptide. The tripeptide can have any other amino acids following it, except 'P'. I extracted them with the following way. from Bio import SeqIO RGD = [] for record in SeqIO.parse("input.fasta", "fasta"): rgd_count = record.seq ...
fasta pattern matching biopython written 12 months ago by arunprasanna8320 • updated 12 months ago by WouterDeCoster29k
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Comment: C: Confusion in SRA submission
... Wow. Thats cool ! I didn't know about this ! ...
written 13 months ago by arunprasanna8320
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Confusion in SRA submission
... Hello, I am downloading an SRA data for a study. The study is basically, Illumina Paired data. However, the study description shows that, "This run has 2 reads per spot" and Reads section show the following: Reads (separated) \>gnl|SRA|SRR768721.1.1 HWI-ST0798_0099:2:1101:1545:2240 (Biological ...
sra rna-seq written 13 months ago by arunprasanna8320 • updated 13 months ago by genomax49k
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Map fasta headers based on sequence match
... Hello, I am looking for a tool to do the following: I have two fasta files with same sequence content, but the headers have been named differently by different sources. File1: \>head1 examplesequence \>head2 anothersequence File2: \>seq1 examplesequence \>seq2 anothersequence ...
fasta sequence written 13 months ago by arunprasanna8320
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SRA submitted files
... Hello, Can anyone please help me with following doubt ?. Are the fastq files submitted in SRA are trimmed with adapters and QC checked ? or they are raw reads straight from the sequencing ? What is the usual custom followed ? Thanks, AP ...
ngs rna-seq written 14 months ago by arunprasanna8320
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Answer: A: SRA to fastq
... From SRA toolkit => "./fastq-dump SRA*** " ...
written 14 months ago by arunprasanna8320
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Visualization of Motif synteny
... Hello, Is there any viewer that can visualize motif synteny ?. I have discovered motif with weeder. I wish to visualize the order of synteny. Please give your suggestions. Thanks, AP ...
synteny motifs written 16 months ago by arunprasanna8320 • updated 16 months ago by natasha.sernova2.9k

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