bioinformatics

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Running BLAST through XGrid

Does anyone have any experience running BLAST with XGrid? Googling reveals a tool called \'Xgrid BLAST\' existed but not where to ge开发者_开发问答t.BLAST is included with Xgrid. Quoting from \"Utili[详细]

2022-12-20 13:41 分类：问答
python script for robust multi-array average on microarray data

I have tried google with no luck. I have seen some weak references to robust multi-array a开发者_运维百科veraging done with python but no code. I am not so interested in reinventing the wheel. Any sug[详细]

2022-12-20 11:17 分类：问答
running BLAST (bl2seq) without creating sequence files

I have a script that performs BLAST queries (bl2seq) The script works like this: Get sequence a, sequence b[详细]

2022-12-19 18:48 分类：问答
how to rank gene using information gain?

how gene ranking is done for microarray data using information gain and chi-square stati开发者_Go百科stics ?? Please illustrate with a simple example..You could use the open source machine learning so[详细]

2022-12-18 04:28 分类：问答
Draw a colored sphere from cartesian coordinates in pymol

I was looking in 开发者_StackOverflow中文版the wiki how to convert the following information about beads, cartesian coordinates + energy :[详细]

2022-12-16 03:00 分类：问答
Python, Huge Iteration Performance Problem

I\'m doing an iteration through 3 words, each about 5 million characters long, and I want to find sequences of 20 characters that identifies each word. That is, I want to find all sequences of length[详细]

2022-12-14 18:05 分类：问答
How to extract the first hit elements from an XML NCBI BLAST file?

Im trying to extract only the first hit from an NCBI xml BLAST file. next I would like to get only the first HSP. at the final stage I would like to get these based on best score.[详细]

2022-12-14 06:41 分类：问答
Does a regular expression exist for enzymatic cleavage?

Does a regular expression exist for (theoretical) tryptic cleavage of protein sequences? The cleavage rule for trypsin is: after R or K, but not before P.[详细]

2022-12-13 11:31 分类：问答
Fast assessment of corrupted Affymetrix CEL files

I\'m trying to normalize a big amount of Affymetrix CEL files using R. However, some of them appear to be truncated, so when reading them i get the error[详细]

2022-12-12 22:28 分类：问答
multiFASTA file processing

I was curious to know if there is any bioinformatics tool out there able to process a multiFASTA file giving me infos like number of sequences, length, nucleotide/aminoacid content, etc. and maybe aut[详细]

2022-12-12 14:26 分类：问答